I'm just curious since I wanted to get both Clean Hands and Ghost, I just stole her key while using Bend Time level 2 and quickly Blinked to that room upstairs, collected the rune and broke through the wooden planks, all before any music cue and I know for fact upon the level's completion I got both ghost and "didn't kill anyone" ticks...I wanted to avoid any sort of confrontation to not screw these achievements up. I know the game has been patched since December, 4, but I'm just curious: does helping Granny / Slackjaw in Mission 7: The Flooded District affect the ending in ANY way?

I can't remember if there's a blurb about slackjaw or not. I don't think so.

Well, helping granny rags put the rat in the elixer bottles makes a few weepers in the distillery the next mission and raises chaos a good amount. So I assume killing slackjaw for slackjaw soup would also raise it a bit.

I tried my ghost/clean-hands run after the game was patched, but still somehow Granny Rags counted as a detection. In the end I had to do a playthrough without the Granny Rags missions to avoid her encounter later. It felt a bit like cheating though.

Others HAVE reported success after the patch, so your results may be better than mine.

killing either of them grants you an achymant/trophy if your on console, dosent really change the endings though.

Yeah, I don't know if it effects the achievement still after the December 4th patch, but I know that I had to entirely skip the Granny Rags quest in the first mission just to get the clean hands achievement (I did two runs previously that should have garnered me the achievement but instead this little bug ruined it for me, but luckily this game is awesome enough to warrant multiple playthrough's). If you perchance don't get the achievement, I just recommend restarting the game and avoiding the first side quest entirely. I mean, if you speed through the game, it takes maybe 3-5 hours which isn't that long for a 100 gamerscore achievement.