Same here. I attempted to negotiate peace between both sides but ultimately wound up killing him, going against the dialogue choices that I made. I'm starting to think that broke the quest.
I am stuck on this quest. I killed William Wray and now I am supposed to go back to talk to Auntie face to face in her office but I'm not able to use the elevator that takes me up there. Is this a bug or did I miss a step somewhere?