And what was in the room that contained the Doctor's greatest fear? (Room 11, of course.)

I think I know: Amy's grave, or her dead body. The Doctor's greatest fear is that he will cause the deaths of those who care about him. (It's not like it hasn't happened before. Think Adric, for starters.) Hence, his parting of the ways with Amy and Rory at the end of the episode. Hell, he pretty much spelled it out for us during his talk with Amy, with him saying that the only other way it could end would be with him standing over their corpses.

"He's saving us."