if the name The Doctor is supposed to be a promise then trapping billions in a time lock and leaving them to die goes completely against the notion of a doctor doing no harm. got to be the real 9th doctor...
It really is the theory that makes the most sense, but I wouldn't put it past The Moff to try to turn this into something a bit more complicated.
But the dialogue between Hurt and Smith sure make it seem as if Hurt is the real 9th. The name, the promise and what little we know of the Time War... It makes sense.