Well, the Hurt Doctor's activities during the Time War could just have become common knowledge among the Time Lords and thus The Doctor. Though not saying I go along with that theory.
Edit - the more I think of it, the less I like the idea of him being a split off from 8/9. It would more or less be a reprise of Ten(B), the meta-crisis Doctor. The real Doctor may have been angered by 10B's actions but he didn't have to feel shame or guilt over it, as it wasn't 'him' or his 'previous incarnation.' Whereas Eleven clearly felt some sort of shame at Hurt's actions. If it transpires that Hurt is not from the 'real' Doctor lineage, it's just a cop-out. It may as well be a different Time Lord.