Yes, just like the last game you certainly can. However you will get warnings againa nd de-sync if you kill too many in a short amount of time.

you can kill people and every time you do it says Ezio can not harm civilians. If you keep killing the civilians, you will be desychronized

heh heh of course you can! But are you really an assassin if you massacre civilians?

Yeah you can, but don't do it too much. Don't go around and just randomly kill people when your in their way (yes, that also means the beggers and the people who sing to you!) One time I went to do an air assassination, but winded up killing a civilian sitting down lol