During his lifetime, Muhammad(sa) is not known to have murdered anyone. Neither did Prophet Muhammad(sa) give any order to kill Jews. The story, though not proven to be authentic by some scholars, tells us that Jews were given the sentence of death for their treason according to the Jewish Law by the arbiter who was chosen by the said Jews themselves. Their arbiter made this decision with their willing appointment of him, per Biblical law (not Qur’anic law), and for the crime of high treason. Prophet Muhammad(sa) had no say in this matter, and gave no such order.
This is perhaps one of the most common contemporary allegations levied against Prophet Muhammad(sa) . It is also one of the most spurious.
This event occurred after the largest battle ever held on Arabian soil in Medina during Prophet Muhammad’s life. The Confederate Army comprised of no less than 12,000 soldiers while the Muslims barricaded themselves in Medina, along with their sworn allies—per the Charter of Medina—numbering roughly a tenth the size. While the Muslims were victorious, they came within moments of annihilation due to the Banu Quraizah tribe’s treason.
Critics baselessly claim that Prophet Muhammad(sa) blindly executed the entire tribe. This too is baseless. Prophet Muhammad(sa) and the Jews were allies, as enshrined in the Charter of Medina Article 49, which states,
“The parties to this Pact are bound to help each other in the event of an attack on Yathrib.”
The Banu Quraizah Tribe was an equal and willing party to this pact. Yet, in the heat of battle, the Banu Quraizah sided with the enemy against the state of Medina despite their prior signed agreement. Fortunately, the remaining allied Medina army was able to withstand this treasonous act and win the battle against incredible odds. The question remained, however, how to address the Banu Quraizah’s treason. Adding to the dilemma was the fact that the Banu Quraizah had committed this act once before, upon which Prophet Muhammad(sa) merely exiled them. When they later asked his forgiveness, he granted it, which is why they had since re-entered Medina. The 19th century historian Stanley Lane-Poole accurately describes the events that followed the Battle of the Ditch:
Of the sentences on the three clans, that of exile, passed upon two of them, was clement enough. They were a turbulent set, always setting the people of Medina by the ears; and finally, a brawl followed by an insurrection resulted in the expulsion of one tribe; and insubordination, alliance with enemies and a suspicion of conspiracy against the Prophet’s life, ended similarly for the second. Both tribes had violated the original treaty, and had endeavored in every way to bring Muhammad and his religion to ridicule and destruction. The only question is whether their punishment was not too light. Of the third clan a fearful example was made, not by Muhammad, but by an arbiter appointed by themselves. When Quraish and their allies were besieging Medina and had well-nigh stormed the defences, this Jewish tribe [the Banu Quraizah] entered into negotiations with the enemy, which were only circumvented by the diplomacy of the Prophet. When the besiegers had retired, Muhammad naturally demanded an explanation of the Jews. They resisted in their dogged way and were themselves besieged and compelled to surrender at discretion. Muhammad, however, consented to the appointing of a chief of a tribe allied to the Jews as the judge who should pronounce sentence upon them. This chief gave sentence that the men, in numbers some 600, should be killed, and the women and children enslaved; and the sentence was carried out. It was a harsh, bloody sentence; but it must be remembered that the crime of these men was high treason against the State, during a time of siege; and one need not be surprised at the summary execution of a traitorous clan.” 
Thus, Prophet Muhammad did not order any execution, nor did he participate in the execution. On the contrary, Prophet Muhammad graciously agreed to let the Banu Quraizah’s own ally, Sa‘d bin Mu‘adh of Aus, deliver the verdict. Why blame Prophet Muhammad for a decision he did not make and for a crime he did not commit? Adding to the injustice in blaming Prophet Muhammad is the fact that Sa‘d bin Mu‘adh did not deliver his decision based on the Qur’an. Rather, he delivered the judgment for the Banu Quraizah based on the punishment for treason that their book, the Torah, prescribes:
“When thou comest nigh unto a city to fight against it, then proclaim peace unto it. And it shall be, if it make thee answer of peace, and open unto thee, then it shall be, that all the people that is found therein shall be tributaries unto thee, and they shall serve thee. And if it will make no peace with thee, but will make war against thee, then thou shalt besiege it: And when the Lord thy God hath delivered it into thine hands, thou shalt smite every male thereof with the edge of the sword: But the women, and the little ones, and the cattle, and all that is in the city, even all the spoil thereof, shalt thou take unto thyself; and thou shalt eat the spoil of thine enemies, which the Lord thy God hath given thee. Thus shalt thou do unto all the cities which the Lord thy God doth give thee for an inheritance, thou shalt save alive nothing that breatheth: But thou shalt utterly destroy them; namely, the Hittites, and the Amorites, the Canaanites, and the Perizzites, the Hivites, and the Jebusites; as the Lord thy God hath commanded thee: That they teach you not to do after all their abominations, which they have done unto their gods; so should ye sin against the Lord your God.” 
Thus, the Banu Quraizah sealed their own fate, with their own actions, according to their own Book. Prophet Muhammad had nothing to do with it—other than agreeing to let an ally to the Banu Quraizah arbitrate between them, and to bind himself to that arbiter’s decision.
Moreover, no Jewish tribes, Jewish historians, or Jewish scholars record this event. This is shocking because the Jewish people have recorded their history better than perhaps any people in history. Yet, in regards to such a massive execution, every Jewish historian, scholar, and tribe is silent.
Dr. Barakat Ahmad, author of “Muhammad and the Jews,” argues, based on authentic sources from time periods well before Ibn Ishaq, that it is highly probable that no execution took place at all. We gladly invite Wilders, or anyone for that matter, to respond to Dr. Ahmad’s book.
As of now, however, it is clear that Prophet Muhammad committed no wrong against the Banu Quraizah. History records that the Banu Quraizah agreed to a constitution, the Charter of Medina, and that constitution explicitly required loyalty to the state of Medina, particularly in case of attack from an external army. After committing to Medina, the Banu Quraizah violated that loyalty with a treasonous act in the heat of battle. The claimed execution that followed, if it happened, was the result of their choice to commit treason, per the judgment of a judge they demanded, according to the law elucidated in their book. Prophet Muhammad, far from being responsible for any deaths, interceded and even forgave those Jews who asked his forgiveness. To place even the slightest responsibility on anyone but the Banu Quraizah is nothing less than ridiculous.
 Geert Wilders, Marked for Death: Islam’s War Against the West and Me, 39 (2012).
 Stanley Lane-Poole, Studies in a Mosque, 68 (1883) (emphasis added).
 Deuteronomy 20: 10-18.