There appears to be a common theme running through this season, and it's the color scheme of red and blue. We've seen this in Blade Runner. It's also used for the girls in Evangelion. It's also been used in the Lindsay Lohan bomb, I Know Who Killed Me. Using the two opposite colors is used to highlight things. The siren put this foremost in my mind. Rewatching the episode, there are subtle little bits about it. Amy's fingernail polishes switches between colors. So does the Doctor's tie. Amy's Schrodinger pregnancy. There are definitely two timelines here, with two Doctors running around.
I am about to take a WAG (Wild Ass Guess) what is happening here.
The second timeline is the timeline from Classic Who, the old episodes from the days of William Hartnell up to McGann. The Doctor that is doing to die is the one from that timeline, effectively severing everything. After all, if the current timeline is the only one, why does the Doctor still have the Time Lord summoning cube from the end of War Games (Gaiman has said we would see something from Who continuity we haven't seen in ages). There have been rumors that the Time Lords will be appearing sometime this season. What if the two timelines are threatening to merge, destabilizing everything? And the other Doctor, seeing as how there can be only one, wants to make sure that one is him?