Is the clean hands achievement bugged for dishonored

No, but it has a condition attached. It's not enough to just go back and redo missions to get no kills, for example if you played missions 1 to 9 but killed someone in mission 4, you would not get the achievement if you redid mission 4 with no kills, even though now all your stats show as no kills.

What you have to do is play through each mission in turn and get no kills. So in the above case you'd have to play 1 -3, then when 4 says you killed someone, redo it without advancing to 5, and then do 5 - 9 without killing anyone. Only then will the achievement be granted.