User blog comment:Rainb0wSprinklz/Problems with the final confrontation between Granny Rags and Slackjaw/@comment-5469467-20121231032159

I had this problem as well, and I had thought I finished the game without killing anyone (Granny Rags included). A patch was released on Steam a few weeks ago, with one of the features being that it fixed the Granny Rags encounter not registering as non-lethal. After the patch, I reloaded a save at the very end of the last level, and quickly finished the game. Sure enough, the "Clean Hands" achievement registered.

This was all on PC, so I'm not sure if similar patches are on consoles yet. Regardless; the devs know where the problem is, and can fix it.