Holy shit! What an episode! That was the best episode yet. I love the references to video games with weapon upgrades and even an "easter egg." I'm still going with William being the Man in Black. In the scene with Bernard and Dolores, it's never actually revealed that she ran away to the camp where she ran into William, she just says she ran away. It could have been from an earlier loop, and not necessarily from the present time line. Also, the more I think about it, the more I'm thinking that what the Man in Black wants (if it really is William) is to find a way to get Dolores out of the park, and the maze is the answer to freeing her (kinda like a modern day Pinocchio). If you think about it, it never really shows the MIB raping her when he takes her into the barn. My guess now is, he didn't assault her, but rather placed the gun into the hay which she then used when she shot the bandit (again, going with the theory that they're showing things not in chronological order and that they are using flashbacks to fuck with the audience).
But that's just my theory...