The Qaynuqa withdrew inside the fort which was their refuge. They probably believed that their friends and allies in Medina would intercede for them and that the matter would be settled with some indemnities on both sides. But Muhammad meant to make the most of the incident. He sent his private army to blockade the tower and prevent the Jews from taking in supplies of food. Several Medinan allies of the Qaynuqa abandoned them and took sides against them, loyalty to the cause taking precedence over their sworn word. The other Jewish tribes, ofr one reason or another, failed to intervene. Probably they, too, put their faith in mediation; and the various Jewish groups may well have had differences of their own. The blockade lasted for fifteen days before the defenders gave in. Muhammad wanted to put all of them to death; and this time Ibn Ubayy did make a strong move to intercede on behalf of his allies.
As with the destruction of Banu Nadir's orchards and the fields of the city of Taif for which the residents depended on for food, it seems to have been a regular practice for Muhammad to engage in collective punishment against civilians.
As always, I have no problem condemning Muhammad's actions as war crimes and I join any Muslim who also condemns them as war crimes, including shafique.
For some reason, however, I don't think I should hold my breath.