Abu Rafi’ ibn Abi Al-Huqaiq is another person who was killed in the lifetime of Prophet Muhammed (p). The reasons were that he incited others to go to war against the Muslims. He even supplied the enemies of the Muslims with ammunition, and other things needed to go to war against the Muslim community. Hence, the Prophet ordered that he be killed.
Additionally, it seems as though some critics spread misinformation, claiming that Abu Rafi got killed as a result of him writing poetry, and nothing else. However, this is false. The following historical evidences provide sufficient proof that Abu Rafi got killed as a consequence of him being a war-monger, and wanted the Muslim community exterminated.
Narrated Al-Bara bin Azib: Allah’s Messenger sent some men from the Ansar to ((kill) Abu Rafi`, the Jew, and appointed `Abdullah bin Atik as their leader. Abu Rafi` used to hurt Allah’s Messenger and help his enemies against him. He lived in his castle in the land of Hijaz. When those men approached (the castle) after the sun had set and the people had brought back their livestock to their homes. `Abdullah (bin Atik) said to his companions, “Sit down at your places. I am going, and I will try to play a trick on the gate-keeper so that I may enter (the castle).” So `Abdullah proceeded towards the castle, and when he approached the gate, he covered himself with his clothes, pretending to answer the call of nature. The people had gone in, and the gate-keeper (considered `Abdullah as one of the castle’s servants) addressing him saying, “O Allah’s Servant! Enter if you wish, for I want to close the gate.” `Abdullah added in his story, “So I went in (the castle) and hid myself. When the people got inside, the gate-keeper closed the gate and hung the keys on a fixed wooden peg. I got up and took the keys and opened the gate. Some people were staying late at night with Abu Rafi` for a pleasant night chat in a room of his. When his companions of nightly entertainment went away, I ascended to him, and whenever I opened a door, I closed it from inside. I said to myself, ‘Should these people discover my presence, they will not be able to catch me till I have killed him.’ So I reached him and found him sleeping in a dark house amidst his family, I could not recognize his location in the house. So I shouted, ‘O Abu Rafi`!’ Abu Rafi` said, ‘Who is it?’ I proceeded towards the source of the voice and hit him with the sword, and because of my perplexity, I could not kill him. He cried loudly, and I came out of the house and waited for a while, and then went to him again and said, ‘What is this voice, O Abu Rafi`?’ He said, ‘Woe to your mother! A man in my house has hit me with a sword! I again hit him severely but I did not kill him. Then I drove the point of the sword into his belly (and pressed it through) till it touched his back, and I realized that I have killed him. I then opened the doors one by one till I reached the staircase, and thinking that I had reached the ground, I stepped out and fell down and got my leg broken in a moonlit night. I tied my leg with a turban and proceeded on till I sat at the gate, and said, ‘I will not go out tonight till I know that I have killed him.’ So, when (early in the morning) the cock crowed, the announcer of the casualty stood on the wall saying, ‘I announce the death of Abu Rafi`, the merchant of Hijaz. Thereupon I went to my companions and said, ‘Let us save ourselves, for Allah has killed Abu Rafi`,’ So I (along with my companions proceeded and) went to the Prophet and described the whole story to him. “He said, ‘Stretch out your (broken) leg. I stretched it out and he rubbed it and it became All right as if I had never had any ailment whatsoever.” (Sahih al-Bukhari volume 5, Book 59, Hadith 371)
Ṣafi al-Raḥmān Mubarakfuri
Salam bin Abi Al-Huqaiq (Abu Rafi) was a terrible Jew criminal, who had mustered the troops of the Confederates and provided them with a lot of wealth and supplies, on the one hand, and used to malign the Prophet on the other. When the Muslims had settled their affair with Banu Quraiza; Al-Khazraj tribe, a rival of Al-Aws, asked for the Prophet’s permission to kill that criminal in order to merit a virtue equal to that of Al-Aws who had killed another criminal of Jews Ka’b bin Al-Ashraf. The Prophet gave them his permission provided that no women or children be killed. 
Abu Rafe, called also Sallam Ibn Abul Hokeik, was the chief of Bani Nazeer, who had warred with the Moslems at Medina, and had been banished to Khyber. He taken a prominent part in the assembling of most of the Bedioun tribes at the war of the confederates when they besieged Medina. Subsequently, he had excited Bani Fezara and other Bedioun tribes to carry on their depredations among the Moslems. A band of the latter was dispatched to inflict condign punishment upon him, and he met with his death at their hands. … 
Maulana Muhammad Ali:
The Bani Nadir, a Jewish tribe, originally lived at Madinah and were in alliance with the Holy prophet, but being suspected of keeping up correspondence with the Quraish, and one of the Arab tribes in alliance with them having murdered some Muslims treacherously, they were asked to renew the alliance, which they refused, and were ultimately banished from Madinah. They settled at Khaibar, a Jewish stronghold and became a source of immense trouble to Muslims, constantly inciting the tribes around Madinah to commit depredations on the Muslims. Abu Huqaiq, their head, was also a leader in the ‘battle of the allies’ in which the Arabian and Jewish tribes had gathered together to give a crushing blow to Islam. Abul Huqaiq and the Jews had thus come out into the field of battle against the Muslims, and even after the allies had to go back in discomfiture, Abul Huqaiq continued to excite and help the Arab tribes living around Madinah in their depredations against the Muslims. The Holy Prophet was thus justified in sending an expedition against the Khaibar Jews, but before doing this in the 7th year, he sent a small party to deal with Abul Huqaiq alone in 6 A.H. Undoubtedly the underlying idea was that bloodshed might be avoided, as far as possible, and that if the ring-leader was taken away, the mischief might cease. But even Abul Huqaiq’s death did not bring peace to the Muslims, and, accordingly, Khaibar had ultimately to be attacked and conquered. That the party sent against him chose to adopt the method which was successfully adopted against Ka’b, again throws no blame on the Prophet. 
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 Sealed Nectar By Ṣafi al-Raḥman Mubarakfuri page 325
 A Critical Exposition of the Popular Jihad (Original 1885) – Cheragh Ali page 71 – 72
 Muhammad the Prophet: by Maulana Muhammad Ali page 207