Alright, guys, this is going to sound a bit out there but I'm proposing another theory that I think might actually be plausible that no one's really talked about.
Throughout series 5 and 6, there are very thinly veiled references to Omega. Omega is one of the founders of Time Lord society, and was thrown into a parallel universe after collapsing a star and inventing time travel. Whilst being stuck in this parallel universe (the antimatter universe), Omega went absolutely insane, and gained total control over this universe. This was the plot of the Three Doctors, the first multi-Doctor special, in which the three Doctors united to take on Omega in his antimatter universe. He was stopped, but it was left very vague.
Here's where my theory comes in. Omega had a sort of device that replicated DNA. In the classic series, he was trying to get the Doctor's DNA in order to have a body in which to exist in, as he was no longer anything but a body of armor. His biodata replicator worked later on in the serial Arc of Infinity, when he replicated himself as the Fifth Doctor. The body then began to dissolve, and once again he was defeated by the Doctor.
Moffat has stated before that he wanted to recreate or assume the feel of "The Three Doctors" again, and subsequently we see references to Omega throughout this entire Silence arc. The soldiers in "A Good Man Goes to War" bear the Omega symbol, and the Omega symbol is also used sparingly throughout other places, such as upon doors and on River Song's jacket at one point in series 5.
So, what could this all mean? I'm thinking perhaps John Hurt is playing the Doctor, but also playing Omega. Omega has perfected his biodata replicator and has replicated the Doctor's DNA perfectly to the point where the Doctor believes it is truly himself. So why is he inside the Doctor's timestream, then, Heretic? Well, that is a bit shaky but I'm thinking maybe a few things could explain it. If he had replicated himself as the Doctor and gone into the Doctor's past, perhaps even to the Time War, then the Doctor would have recognized him as a future version of himself, or something along those lines (I'm imagining the Doctor giving the JH Doctor a scan with his screwdriver and being like, "yep, he's me!") and then the JH Doctor doing something absolutely horrid and then disappearing.
Another theory is perhaps he also entered into the Doctor's timestream a la the GI and Clara, but being the Doctor replicate, wasn't split into millions of pieces and is attempting to claim the Doctor's life for himself. Omega was always very angry and jealous and wanted to become the Doctor so he could remain in this universe due to needing Gallifreyan DNA, so I have a feeling that Omega has been behind the scenes this entire time manipulating the Doctor and drawing him towards a terrible fate which he will have to overcome with the help of Tennant in the 50th. I can see the JH Doctor teaming up with Tennant and Smith (further proved by Tennant and Smith in a clip where they said a third party watched the two's interactions with bemusement and the fact that JH revealed he was partaking in a "trinity" with the Doctors) and then 10 and 11 discovering that this Doctor is not truly the Doctor, and having to stop his grand scheme.
Omega could have engineered the Silence to stop the Doctor or to kill him, and could have been leading behind the scenes the entire time.
In an even crazier theory, maybe the Doctor was split into two regenerations during the Time War-- as he regenerated into 9, his use of The Moment or whatever else he did to Time Lock Gallifrey split him into two incarnations. After committing his unspeakable horror, maybe the Doctor locked him inside his own timestream, and Omega engineered the entire events of The Name of the Doctor in order to cause the timestream to be opened, allowing the JH Doctor to escape.
I don't know. Just some interesting speculation, and I know Moffat has some sort of grand arc behind all of this, and the fact that Omega is a classic anniversary special Big Bad. The signs from earlier hint to it, and while I am almost positive that Omega will be the antagonist, how is still where I'm speculating-- either he's Doctor Hurt, or he's using Doctor Hurt for something terrible.
Whaddya think, Who fans?