In the game, each time you find a Little Sister, you must choose between setting her free or killing her. The story explains that this choice is a moral one: graciously set the Little Sisters free and receive a minimal reward, or kill them to selfishly maximize your reward.
|Image from gamersyde.com|
(The blur in the video is because the character is poisoned or something like that:)
Most enemies in the game are, well, not really villains, just British or Patriot troops that you piss off somehow. I tried to play by Connor's personality and just beat them up to get them off my back, but once again, Connor snapped a few necks. That isn't the end of the world, but later the dissonance really kicked in.
Hopefully designers will start focusing a bit more on thematic unity to avoid embarrassing dissonance. I think it's an important factor of a game experience that needs to be taken seriously.