I think there's a 'flesh' Doctor, and either he gets killed by River, or replaces him when he does. They made a big song and dance about how the flesh Doctor was the same/as good as, no really actually as god as, Amy couldn't tell the difference, all memories shared etc. Then they did this kind of 'oh, who knows if the flesh Doctor is <i>really</i> gone?' at the end of that episode.
That's the only theory I have about his death.