The writers/producers of DW S6 have now achieved something I thought could not happen...
They've made me dislike Rory. Really dislike him.
In that scene in the TARDIS at the end, when the Doctor told Rory to get away from Amy, he had no idea what was going on; all he could see was that suddenly the Doctor had gone very, very scary and threatening towards Amy, and Amy was terrified. His wife was scared stiff.
And what does Rory do? Instead of protecting her, he steps away from her, following the Doctor's order instead of taking care of his wife. He essentially abandons Amy - whom he had no reason to believe was anything other than his wife, and even if he did for some reason suspect that she was a clone/doppleganger, hadn't he just spent the entire two episodes protecting another ganger from humans wanting to kill her? He abandons his wife, letting the Doctor kill her.
I'm not going to get into the arguments I've seen around my flist about whether Amy was a 'ganger' in the same way as the gangers in the episodes, or whether the Doctor really killed her or was doing the only thing he could do to connect with the real Amy. I'm willing to be convinced of his good intentions, though I wish the episode had been clearer on this rather than stressing so much that a ganger could be the same as a human and have equal right to live. The point here is not whether the Doctor actually killed her or not; it's what Rory saw and how it compares to his experiences in the episode. How would he know whether doppleganger-Amy is the same or different from the Jennifer-gangers he was protecting?
He didn't know. He just abandoned the woman he thought was his wife, when she was crying and obviously terrified.
In that two minutes, the writers just committed character assassination on the only character in current Who that I actually like. Well, thanks very much.