It has to be one of the original 12. Who cares whether or not it he included himself.
Just think about it for a second. He first suspected it to be one of the group, then when he found out he said "of all the them, i never thought it would be you". That statement implies that it was indeed one of "them". It was one of the people who he suspected, and he suspected the rest of the 12.
If it was Nathan, would he have said that? That statement wouldn't make the least bit of sense if it was Nathan or Peter or someone like that. It was one of "them", with "them" being the people him and Angela just discussed as being one of the killers.
Addionally it cant be Ma Patrelli, since he'd just spoken to her and his reaction would have likely been a bit different. It's probably not anyone we thought was dead, since he also would've reacted differently. It's almost certainly someone we haven't met, or have met but didn't know was part of the group (Sammy Jenkis, Kensei, etc.)