At last Saturday's 11th Hour Convention Matt Smith said that his debut story has a clue to Amy's departure from the TARDIS. Here is Matt Smith's quote.
“There’s something coming up in the final days of the Ponds that was in The Eleventh Hour…there’s a shot in that. [Moffat's] been thinking about it that long. He always knew how she was going to… I’m saying too much already.”So I guess we should all watch the 11th Hour again and try and find out what that clue is. My guess is the duckpond with no ducks. Just kidding about the duckpond but you never know.