I'm thinking it really was Linderman, Candice was probably still with Micah and it kind of suits the story more with Linderman dying.
Hiro changed the timeline so Peter isn't the bomb (either Sylar is or there is no bomb - I'm guessing there wont be one), the whole Linderman story is him trying to blow up New York so with him dying it ends the story so a new one can unfold.