Firstly: 

Allah, may He be exalted, says (interpretation of the meaning): “And We have sent you (O Muhammad ) not but as a mercy for the Aalameen (mankind, jinns and all that exists)” [al-Anbiya’ 21:107]. The scholars differed concerning the ‘Aalameen (translated here as “mankind, jinns and all that exists”; also often translated as “the worlds”) to whom the Prophet (blessings and peace of Allah be upon him) was sent as a mercy. 

Ibn Jibreen (may Allah have mercy on him) said: 

Here Allah, may He be exalted, says to His Prophet Muhammad (blessings and peace of Allah be upon him): We have not sent you, O Muhammad, to Our creation except as a mercy to those to whom We have sent you of Our creation. 

Then the commentators differed as to the meaning of this verse: does it mean as a mercy to all of the world to whom Muhammad was sent, believers and disbelievers alike? Or does it mean to the believers only and not the disbelievers? 

Some of them said that what is meant is to all the world, both believers and disbelievers. 

It was narrated that Ibn ‘Abbaas said: As far as the one who believes in Allah and the Last Day is concerned, mercy will be decreed for him (by virtue of the Prophet (blessings and peace of Allah be upon him)) in this world and the Hereafter; as for the one who does not believe in Allah and His Messenger, he will be saved (by virtue of the Prophet (blessings and peace of Allah be upon him)) from the punishments that befell the previous landslides and being pelted with stones from heaven. 

Others said that what is meant is he is a mercy to the believers only, to the exclusion of the disbelievers. 

The more correct of the two opinions is that which was narrated from Ibn ‘Abbaas, which says that Allah sent His Prophet Muhammad (blessings and peace of Allah be upon him) as a mercy to all the world, both believers and disbelievers. As for the believers, Allah guided them through him and caused them, through their belief in him and their acting upon what he brought from Allah, to enter Paradise. As for the disbelievers, by virtue of him He warded off from them the hastening of the punishment that came upon the nations who disbelieved in their Messengers before him.

End quote from Tafseer at-Tabari, 18/551-552. See also Tafseer Ibn Katheer, 5/385; Tafseer as-Sa‘di, p. 532 

Ibn Hajar al-Haytami (may Allah have mercy on him) said: 

In the sending of the Prophet (blessings and peace of Allah be upon him) there is mercy even for his enemies, in that the punishment will not be hastened for them.

End quote from Fataawa al-Hadeethiyyah, p. 34 

One of the things that explained this universal mercy by the sending of our Prophet Muhammad (blessings and peace of Allah be upon him) is the verse in which Allah says (interpretation of the meaning):

“And (remember) when they said: ‘O Allah! If this (the Qur’an) is indeed the truth (revealed) from You, then rain down stones on us from the sky or bring on us a painful torment.’

And Allah would not punish them while you (Muhammad ) are amongst them, nor will He punish them while they seek (Allah’s) Forgiveness.”

[al-Anfaal 8:32-33]. 

Shaykh Muhammad Rasheed Rida (may Allah have mercy on him) said: 

It was not in accordance with Allah’s way or laws, or His mercy or wisdom, to punish them when you, O Messenger, are among them; rather He sent you as a mercy to the worlds and as a blessing, not as a punishment. Moreover it was not His way to punish those like them who rejected the Messengers when they were still among them. Rather He would first bring them (His Messengers) out from among them as Ibn ‘Abbaas said. 

End quote from Tafseer al-Manaar, 9/545 

Think about this story that highlight the attitude of the Prophet of mercy (blessings and peace of Allah be upon him) when the people of at-Taa’if rejected him and harmed him severely, when all he was doing was calling them to believe in the Oneness of Allah, and he did not want anything from them apart from that. 

Al-Bukhaari (3231) and Muslim (1795) narrated that ‘Aa’ishah (may Allah be pleased with her), the wife of the Prophet (blessings and peace of Allah be upon him) said to the Prophet (blessings and peace of Allah be upon him): Was there ever a day that was worse for you than the day of Uhud? He said: “I suffered at the hands of your people, and the worst that I suffered from them was the day of al-‘Aqabah, when I presented myself to Ibn ‘Abd Yaleel ibn ‘Abd Kulaal, and he did not respond to what I wanted. So I went, with signs of distress on my face, and I did not recover until I was in Qarn al-Tha’aalib, where I lifted my head and saw that a cloud was shading me. I looked and saw therein Jibraa’eel (peace be upon him), who called me and said: Allaah has heard what your people said to you, and how they have rejected you. He has sent to you the angel of the mountains, so that you can tell him to do whatever you want to them. Then he called the angel of the mountains to me and he greeted me with salaam, then said: O Muhammad, Allaah has heard what your people have said to you, and I am the angel of the mountains. Your Lord has sent me so that you can tell me what to do. What do you want? If you wish I will bring together the two mountains of Makkah to crush them. The Messenger of Allaah (blessings and peace of Allah be upon him) said to him: “Rather I hope that Allaah will bring forth from their loins people who will worship Allaah alone, not associating anything with Him.” 

Secondly: 

More than one of the scholars have stated that the Prophet (blessings and peace of Allah be upon him) did not kill anyone with his own hand except Ubay ibn Khalaf, whom he killed on the day of Uhud. 

Shaykh al-Islam (may Allah have mercy on him) said: 

The Prophet (blessings and peace of Allah be upon him) was the most perfect of people in terms of his courage that is required of leaders in war, but he did not kill anyone with his hand except Ubay ibn Khalaf, whom he killed on the day of Uhud. He did not kill anyone else with his own hand before or after that. 

End quote from Minhaaj as-Sunnah an-Nabawiyyah, 8/57 

Perhaps Allah, may He be exalted, intended the severest punishment for this wretch, so He decreed that he should be killed at the hands of the Prophet (blessings and peace of Allah be upon him), for he was one of the most hostile of people towards him and his religion. Al-Bukhaari (4076) narrated  that Ibn ‘Abbaas (may Allah be pleased with him) said: “Allah becomes extremely angry with the one who is killed by a Prophet and the anger of Allah became severe against the one who caused the face of the Messenger of Allah (blessings and peace of Allah be upon him) to bleed. 

Ahmad (3858) narrated from Ibn Mas‘ood (may Allah be pleased with him) that the Messenger of Allah (blessings and peace of Allah be upon him) said: “The most severely punished of people on the Day of Resurrection will be a man who was killed by a Prophet or who killed a Prophet, or a leader of misguidance or an image maker.”

Classed as saheeh by al-Albaani in as-Saheehah, 281 

Thirdly: 

There is no doubt that, although the Messenger of Allah (blessings and peace of Allah be upon him) did not kill anyone with his own hand except this wretch, he is the one who prescribed and enjoined jihad and urged the Muslims to go out on jihad. There is no contradiction between the fact that he prescribed and enjoined jihad and killed that wretch or anyone else, and the words of Allah, may He be exalted, (interpretation of the meaning) “And We have sent you (O Muhammad ) not but as a mercy for the Alameen (mankind, jinns and all that exists)” [al-Anbiya’ 21:107], because Allah, may He be exalted, only sent him to bring people forth from darkness to light, and to guide them to His straight path. He prescribed for him jihad for His sake and to fight His enemies who wanted to extinguish the light of Allah and spread mischief on earth. 

Allah, may He be exalted, says (interpretation of the meaning): 

“O Prophet (Muhammad )! Strive hard against the disbelievers and the hypocrites, and be harsh against them, their abode is Hell, – and worst indeed is that destination”

[at-Tawbah 9:73] 

“O Prophet (Muhammad )! Urge the believers to fight”

[al-Anfaal 8:65]. 

Jihad for the sake of Allah and fighting the enemies of Allah were among the greatest means of spreading this religion and bringing people out from the darkness of kufr to the light of faith. This is the greatest mercy that people can attain: that Allah saves them from kufr and guides them to faith, and brings them out of darkness into light. 

Because of this mercy (resulting from jihad), which people may not realize, our Lord was amazed at it (this mercy), as it says in the hadeeth.  

It was narrated that Abu Hurayrah said: I heard the Messenger of Allah (blessings and peace of Allah be upon him) say: “Our Lord, may He be glorified and exalted, is amazed with a people who are led into Paradise in chains.”

Narrated by [Abu Dawood, no. 2677] 

In the commentary on the verse in which Allah says (interpretation of the meaning): “You (true believers) are the best of peoples ever raised up for mankind” [Aal ‘Imraan 3:110], Abu Hurayrah (may Allah be pleased with him) said: “You are the best of people for people, you bring them with chains on their necks until they enter Islam.”

Narrated by al-Bukhaari, 4557 

Think about the mercy of the Most Merciful of those who show mercy, Whose mercy no one can describe, the extent of which no one can comprehend. Glory be to Him, His slaves cannot comprehend Him; He is more merciful to His slaves than a mother to her child, as His Prophet (blessings and peace of Allah be upon him) told us. Yet despite that He tests them with calamities and trials, by His wisdom, and He punishes His enemies with vengeance and humiliation in this world and with eternity in Hell in the Hereafter, and none of that contradicts the perfection of His mercy towards His slaves, glory be to Him.

Firstly: 

Allah, may He be exalted, says (interpretation of the meaning): “And We have sent you (O Muhammad ) not but as a mercy for the Aalameen (mankind, jinns and all that exists)” [al-Anbiya’ 21:107]. The scholars differed concerning the ‘Aalameen (translated here as “mankind, jinns and all that exists”; also often translated as “the worlds”) to whom the Prophet (blessings and peace of Allah be upon him) was sent as a mercy. 

Ibn Jibreen (may Allah have mercy on him) said: 

Here Allah, may He be exalted, says to His Prophet Muhammad (blessings and peace of Allah be upon him): We have not sent you, O Muhammad, to Our creation except as a mercy to those to whom We have sent you of Our creation. 

Then the commentators differed as to the meaning of this verse: does it mean as a mercy to all of the world to whom Muhammad was sent, believers and disbelievers alike? Or does it mean to the believers only and not the disbelievers? 

Some of them said that what is meant is to all the world, both believers and disbelievers. 

It was narrated that Ibn ‘Abbaas said: As far as the one who believes in Allah and the Last Day is concerned, mercy will be decreed for him (by virtue of the Prophet (blessings and peace of Allah be upon him)) in this world and the Hereafter; as for the one who does not believe in Allah and His Messenger, he will be saved (by virtue of the Prophet (blessings and peace of Allah be upon him)) from the punishments that befell the previous landslides and being pelted with stones from heaven. 

Others said that what is meant is he is a mercy to the believers only, to the exclusion of the disbelievers. 

The more correct of the two opinions is that which was narrated from Ibn ‘Abbaas, which says that Allah sent His Prophet Muhammad (blessings and peace of Allah be upon him) as a mercy to all the world, both believers and disbelievers. As for the believers, Allah guided them through him and caused them, through their belief in him and their acting upon what he brought from Allah, to enter Paradise. As for the disbelievers, by virtue of him He warded off from them the hastening of the punishment that came upon the nations who disbelieved in their Messengers before him.

End quote from Tafseer at-Tabari, 18/551-552. See also Tafseer Ibn Katheer, 5/385; Tafseer as-Sa‘di, p. 532 

Ibn Hajar al-Haytami (may Allah have mercy on him) said: 

In the sending of the Prophet (blessings and peace of Allah be upon him) there is mercy even for his enemies, in that the punishment will not be hastened for them.

End quote from Fataawa al-Hadeethiyyah, p. 34 

One of the things that explained this universal mercy by the sending of our Prophet Muhammad (blessings and peace of Allah be upon him) is the verse in which Allah says (interpretation of the meaning):

“And (remember) when they said: ‘O Allah! If this (the Qur’an) is indeed the truth (revealed) from You, then rain down stones on us from the sky or bring on us a painful torment.’

And Allah would not punish them while you (Muhammad ) are amongst them, nor will He punish them while they seek (Allah’s) Forgiveness.”

[al-Anfaal 8:32-33]. 

Shaykh Muhammad Rasheed Rida (may Allah have mercy on him) said: 

It was not in accordance with Allah’s way or laws, or His mercy or wisdom, to punish them when you, O Messenger, are among them; rather He sent you as a mercy to the worlds and as a blessing, not as a punishment. Moreover it was not His way to punish those like them who rejected the Messengers when they were still among them. Rather He would first bring them (His Messengers) out from among them as Ibn ‘Abbaas said. 

End quote from Tafseer al-Manaar, 9/545 

Think about this story that highlight the attitude of the Prophet of mercy (blessings and peace of Allah be upon him) when the people of at-Taa’if rejected him and harmed him severely, when all he was doing was calling them to believe in the Oneness of Allah, and he did not want anything from them apart from that. 

Al-Bukhaari (3231) and Muslim (1795) narrated that ‘Aa’ishah (may Allah be pleased with her), the wife of the Prophet (blessings and peace of Allah be upon him) said to the Prophet (blessings and peace of Allah be upon him): Was there ever a day that was worse for you than the day of Uhud? He said: “I suffered at the hands of your people, and the worst that I suffered from them was the day of al-‘Aqabah, when I presented myself to Ibn ‘Abd Yaleel ibn ‘Abd Kulaal, and he did not respond to what I wanted. So I went, with signs of distress on my face, and I did not recover until I was in Qarn al-Tha’aalib, where I lifted my head and saw that a cloud was shading me. I looked and saw therein Jibraa’eel (peace be upon him), who called me and said: Allaah has heard what your people said to you, and how they have rejected you. He has sent to you the angel of the mountains, so that you can tell him to do whatever you want to them. Then he called the angel of the mountains to me and he greeted me with salaam, then said: O Muhammad, Allaah has heard what your people have said to you, and I am the angel of the mountains. Your Lord has sent me so that you can tell me what to do. What do you want? If you wish I will bring together the two mountains of Makkah to crush them. The Messenger of Allaah (blessings and peace of Allah be upon him) said to him: “Rather I hope that Allaah will bring forth from their loins people who will worship Allaah alone, not associating anything with Him.” 

Secondly: 

More than one of the scholars have stated that the Prophet (blessings and peace of Allah be upon him) did not kill anyone with his own hand except Ubay ibn Khalaf, whom he killed on the day of Uhud. 

Shaykh al-Islam (may Allah have mercy on him) said: 

The Prophet (blessings and peace of Allah be upon him) was the most perfect of people in terms of his courage that is required of leaders in war, but he did not kill anyone with his hand except Ubay ibn Khalaf, whom he killed on the day of Uhud. He did not kill anyone else with his own hand before or after that. 

End quote from Minhaaj as-Sunnah an-Nabawiyyah, 8/57 

Perhaps Allah, may He be exalted, intended the severest punishment for this wretch, so He decreed that he should be killed at the hands of the Prophet (blessings and peace of Allah be upon him), for he was one of the most hostile of people towards him and his religion. Al-Bukhaari (4076) narrated  that Ibn ‘Abbaas (may Allah be pleased with him) said: “Allah becomes extremely angry with the one who is killed by a Prophet and the anger of Allah became severe against the one who caused the face of the Messenger of Allah (blessings and peace of Allah be upon him) to bleed. 

Ahmad (3858) narrated from Ibn Mas‘ood (may Allah be pleased with him) that the Messenger of Allah (blessings and peace of Allah be upon him) said: “The most severely punished of people on the Day of Resurrection will be a man who was killed by a Prophet or who killed a Prophet, or a leader of misguidance or an image maker.”

Classed as saheeh by al-Albaani in as-Saheehah, 281 

Thirdly: 

There is no doubt that, although the Messenger of Allah (blessings and peace of Allah be upon him) did not kill anyone with his own hand except this wretch, he is the one who prescribed and enjoined jihad and urged the Muslims to go out on jihad. There is no contradiction between the fact that he prescribed and enjoined jihad and killed that wretch or anyone else, and the words of Allah, may He be exalted, (interpretation of the meaning) “And We have sent you (O Muhammad ) not but as a mercy for the Alameen (mankind, jinns and all that exists)” [al-Anbiya’ 21:107], because Allah, may He be exalted, only sent him to bring people forth from darkness to light, and to guide them to His straight path. He prescribed for him jihad for His sake and to fight His enemies who wanted to extinguish the light of Allah and spread mischief on earth. 

Allah, may He be exalted, says (interpretation of the meaning): 

“O Prophet (Muhammad )! Strive hard against the disbelievers and the hypocrites, and be harsh against them, their abode is Hell, – and worst indeed is that destination”

[at-Tawbah 9:73] 

“O Prophet (Muhammad )! Urge the believers to fight”

[al-Anfaal 8:65]. 

Jihad for the sake of Allah and fighting the enemies of Allah were among the greatest means of spreading this religion and bringing people out from the darkness of kufr to the light of faith. This is the greatest mercy that people can attain: that Allah saves them from kufr and guides them to faith, and brings them out of darkness into light. 

Because of this mercy (resulting from jihad), which people may not realize, our Lord was amazed at it (this mercy), as it says in the hadeeth.  

It was narrated that Abu Hurayrah said: I heard the Messenger of Allah (blessings and peace of Allah be upon him) say: “Our Lord, may He be glorified and exalted, is amazed with a people who are led into Paradise in chains.”

Narrated by [Abu Dawood, no. 2677] 

In the commentary on the verse in which Allah says (interpretation of the meaning): “You (true believers) are the best of peoples ever raised up for mankind” [Aal ‘Imraan 3:110], Abu Hurayrah (may Allah be pleased with him) said: “You are the best of people for people, you bring them with chains on their necks until they enter Islam.”

Narrated by al-Bukhaari, 4557 

Think about the mercy of the Most Merciful of those who show mercy, Whose mercy no one can describe, the extent of which no one can comprehend. Glory be to Him, His slaves cannot comprehend Him; He is more merciful to His slaves than a mother to her child, as His Prophet (blessings and peace of Allah be upon him) told us. Yet despite that He tests them with calamities and trials, by His wisdom, and He punishes His enemies with vengeance and humiliation in this world and with eternity in Hell in the Hereafter, and none of that contradicts the perfection of His mercy towards His slaves, glory be to Him.