Okay, I just watched the last five minutes again and after listening to the exchange between Doctor Hurt and Doctor Smith, now I'm not so sure that he's the Doctor in his original form, but rather the 9th. The dialogue does seem to point to an unseen regeneration where he had already taken the name 'The Doctor', but did things that were totally out of line with his moral compass. Perhaps he was so mortified by his actions that he even forced himself to regenerate after that, becoming Eccleston and trying to go back to the type of person he had been prior to the Time War.
I'm just guessing here, but now that I've watched that scene again, I think that perhaps it really does make more sense than an earlier version. And hey, 'The Ninth Doctor' would make a cool title for the November show.