I really do think a lot of people seem to miss the point of Amy taking Rory’s name in The God Complex. It wasn’t a commentary on gender politics, or anything like that. It was to show a balance in their relationship. In season 5 Rory took the name Rory Pond. Here Amy finally took the name Amy Williams. By taking the name Williams, Amy mirrored Rory, and so their relationship became balanced.
According to Toby Whithouse, the Doctor refers to Amy as ‘Amy Williams’ in The God Complex because he is finally accepting that she’s married (and therefore unavailable for him to have a romantic relationship with, I think the implication was).
Steven Moffat has said that Rory took Amy’s name, though (in a Radio Times interview) and so has Arthur Darvill. I’ll be really disappointed if that’s forgotten.
As for the names on the divorce papers- something is terribly fishy there. They’re dated ‘2012’, for a start, when the Whoniverse is a year ahead of us. I assume that either a) they were filled out by a random props guy (who assumed that the wife of Rory Williams would be Amy Williams) and won’t actually be shown fully on screen, or b) something strange really is going on and this is alternate-universe Rory and Amy or something.