Not sure if everybody already knows but you can still kill civilians and the limit before desynchronization is still 3 in quick succesion. A rumor went around that you couldn't attack them at all because the prompt didn't appear. The prompt indeed doesn't appear and you can't just attack them by pressing a button like you would with a soldier. I was just messing around with the bow however and Connor suddenly shot a civilian giving me the "Warning: Your ancestor did not kill civilians or domestic animals" message. After messing around with that some more I found out that with certain tools you can "accidentally" hit civilians. If you lock on to a civilian, however, you can always use any weapon/tool to attack or kill them. So the option is still there and you can use anything you want, you just need to be locked on (you can also assassinate them on the move). The message also seems to imply you can do the same to domestic animals (not that it has any use). In short: if you lock on you can do anything you could with a soldier.

Just thought I'd let you guys know.