So after I strike the deal with Slackjaw in Mission 3, I come out to find that the Weepers who exist as a result of what I did are loose and they run over and kill a few people. Does anybody know if this counts against me for the achievement? I apologize if this has already been asked, but I couldn't find it.

I read somewhere that doing the granny rags stuff screws up the clean hands achievement especally the still. It's best to not doing anything with her at all b/c even if it's checked off as no kill you still might not get it.

Now I don't know how true it is, I just didn't do any granny rags stuff on my clean hands/ghost playthrough.

But... But... Precious Runes :'c

i did all her things on the 2nd mission and got a clean play/no kill/no alert. the only hard part about it was the 3 men knocking and getting lucky enough so they would not be looking at the window and each other somehow. sleep dart as fast as you can so they dont look at bodies or else it will increase they're alert bar and if they see you in the window you basically failed.

No, it's not the still. There's an encounter with her much, much later, in Chapter 7, where even if you take her out non-lethally you lose out on Clean Hands. I don't feel like getting into the details, but it does make a sort of sense. However, it's very much a technicality kind of thing and quite annoying considering the game will let you get away with poisoning the still.