How about this for speculation (purely, don't worry, no actual spoilers here. This is straight out of my head), to fit in with Kens statements about the ending:
It's a recurring theme throughout the game that, due to her extended time in captivity, Elizabeth has very serious trust issues. This is presented to the player in various detail throughout the game until it's a prevailing theme.
Everything happens as it should, Booker and Elizabeth escape the city, and then when it's finally certain that they're both safe for good, Elizabeth kills Booker (first person perspective, facing Elizabeth and possibly with a gun pointed at you) because, even after everything they had been through, she still couldn't bring herself to trust him. Fade to black, credits roll.