Except that in Let's Kill Hitler, they know that River=Melody, which Amy references again when the Doctor drops them off.

No, I'm just trying to understand how this can make sense, even in a Doctor Who way. Are we in a loop? Was there just some cinematic sleight-of-hand? It seems kind of important that Amy and Rory are only now put into the circumstances that began the season. I'm sure it's intentional, I'm just trying to figure out what…

Okay, so…

I'm glad I'm not the only one who cried at that moment.

I've only watched NuWho, but what made this work so well for me is that none of the morality was whitewashed, and I'm not really sure we've seen that in Doctor Who before, at least not this way.