You sound as if these jews were innocent people grazing their cows in field and Prophet Muhammed killed them.
First of all - They are not general Jews-they are just one tribe of jews,no harm was done to other jews.
secondly these numbers were exaggerated.
This jewsish tribe called Bani quaiza betrayed the Muslim army after their allegiance of support. what will you get when a support group in a war if found to be aiding the enemy? These jews were given verdict by the judge they themslves chose and given punishmnet according to old testament.This is what war gives and this is how traitors are punsihed.