My problem with the astronaut is that she says when she first met the doctor as a child he knew all about her. So it doesn't work, although I do agree that it is definitely her that shoots him as she says she is in prison for killing a good man.

I like your theory, except that River is clearly a 51st century person, so it means Amy and Rory get stuck there, which I think would be odd.

I don't know, I feel meh about it, killing the doctor off just left me cold.