Part of me really didn't want BaS to end the way it did. Some part of me wished Booker and Comstock weren't the same person. And I think Elizabeth began to feel the same way. In the beginning of BaS, when she'd heal you when you died, she was very rough about it. But the more you died, the more sincere, and almost desperate, she became. I know, deep down inside, she didn't want to kill Booker. I know.