Pillage was the usual practice when a garrison didn't give up, was it not?
Well, apparently so, but it was not necessarily countenanced by commanders of besieging forces. It will be interesting to bear that observation in mind for future discussions.
The point was M. Giscard asserted in his post that the Mongol captains had the occupants of Samarkand killed because they resisted, while this could not be said of Bonaparte.
Further, the prisoners executed after the capture of Jaffa were, in large part, paroled prisoners who had already surrendered once and released. If they took up arms again, according to the 'rules of war' of the period, they were subject to execution if recaptured.
But such measures were not obligatory. It's not as if the paroled soldiers had arrived in Jaffa by individual choice, in defiance of Bonaparte. It might also have been a useful pretext to dispose of 8-900 plus extra mouths, when rations were in short supply.