Dirty Hipsters said:
The worst part is that if you knock someone out and then they're eaten by rats while knocked out it counts as you killing them. A friend of mine was trying to play through the game with no kills and couldn't figure out what kept screwing him over until he released that rats would randomly kill people he knocked out, so from then on every time he knocked someone out he'd pick up their body and move it so that it wasn't laying on the ground. Such a pain in the ass.
I never had a problem with that, but I do have a humorous story of my own.
I was playing a zero-kill play through after I had finished my kill-everyone-and-everything play through and I had gotten through most of the game. I was in the flooded district right before meeting Daud. I blinked up to one of Daud's assassins on a slanted roof and choked him out, and quickly blinked to another before he could spot me. As I choked out the second I happened to turn back to the first body just as it slid off the roof. Rushing over to the edge and looking down I saw the body hit the ground with a crunch.
I knew that this would count as a kill against me, and I considered reloading but then stopped. Of all the coincidences that had to happen to let this poor soul have stood in just the wrong spot so that his unconscious body would roll off the roof we're too astoundingly high that I had to laugh.
I finished a 1-kill play through.
R.I.P faceless nameless assassin.
Edit: on topic; I don't think Dishonored punishes you for killing since I actually liked the bad ending more.