I know Moffat kept saying on his twitter about a very important line in A Good Man Goes To War that would probably be looked at as non-important by fans.
I really think it's the line when the Doctor says "So technically the first time they were on the Tardis together in this version of reality...." It doesn't seem right to me to just put that in there with no reason.
So, what if reality has different versions (goes back to episode 3, with the pirate ship) but they are all reality, they are all real, and the persons themselves are real. No alternate version of themselves but real, with a different turn of events.
Maybe the Doctor does die in this version of reality, but in another one he is still alive. I have no idea what will happen to the characters in this version, and I think I'm gonna stop now because I am starting to get confused and that's really all I had.
Sorry if this idea was posted before, I must have missed it.