I'm doing a Ghost and Clean Hands first playthrough. For the sidequest where you have to poison the Bottle Street Gang's elixir supply, that won't count against Clean Hands, will it?
Wish I could get an answer about my rune question. Glad I could help. I doubt it will or they're really reinforcing the choice and consequence feature in missing a rune from Granny Rags.
Edit: GreyFox is saying it will invalidate it in the other Clean Hands topic. Not sure who's right.