I just figured if he can survive being unplugged while still in the Matrix in the first two films AND the Matrix gets rebuilt, why couldn't he just pull himself back together (or get rebuilt with the Matrix like everone else)?
That's only his Avatar in the Matrix. The films make it perfectly clear to us that whatever happened there couldn't hurt him.

From what I understand, the Matrix Online, supposedly canonical and written by the Wachowskis were going to bring Neo back again.
So theoretically he wasn't dead at the end of the theatrical cut of Revolutions either, we all just didn't play the crappy MMORPG to find out otherwise.