Muhammad was wise enough to have six clans execute two Jews each in order to stop any blood-feuds. The rest of the executions were probably carried out by Muhammad’s fellow Emigrants from Mecca, as the heads and bodies were dragged into trenches in the business district of Medina.
Source: Watt, Muhammad: Prophet and Statesman, p. 174
How did the executioners decide on which boy to slaughter or leave alive? This hadith gives the obvious answer.
Narrated Atiyyah al-Qurazi: I was among the captives of Banu [tribe] Qurayzah. They (the Companions) examined us, and those who had begun to grow hair (pubes) were killed, and those who had not were not killed. I was among those who had not grown hair. (Abu Dawud; see Ibn Ishaq, p. 466)
This next hadith indicates that a woman was delirious. She was killed.
Narrated Aisha . . . No woman of Banu [tribe] Qurayzah was killed except one. She was with me, talking and laughing on her back and belly (extremely), while the Apostle of Allah . . . was killing her people with the swords. Suddenly a man called her name: Where is so-and-so? . . . I asked: What is the matter with you? She said: I did a new act. [Aisha] said: The man took her and beheaded her. [Aisha] said: I will not forget that she was laughing extremely although she knew that she would be killed. (Abu Dawud)