The other reason I don't believe the Impossible Astronaut killing the Doctor was River killing the Good Man was that there's no obvious way that could lead to her being arrested and bunged into Stormhold.

Speaking of Moffat being sneaky, though: It's mentioned in passing in the Confidential that the writing on the side of the crib, which Amy can't read because it's in Gallifreyan, is the Doctor's name -- which means that in addition to trumpeting the answer to River's identity, Moffat's also quietly slipped us the end to the sentence "The only way you could possibly know my name is --"