Well, the takeover messages specifically mentioned that peasants were being killed, though I can't remember it entirely since it's out of my message history by now. Then the scribe report said that population went down by one, I think. Again, this is all by memory, so I might be remembering something wrong.
Shouldn't we assume that if multiple nobles (which the reports Edmund were sent listed more than one noble) are attacking and killing peasants during a takeover that a scribe note would reflect more than 1 death? Or given the game mechanics, we ignore it since we know it takes a while for actual depopulation?