i think isaac sacrificed himself to create a path to sylar's defeat. after all, he's the future boy. maybe he knew he had to die for sylar to be defeated. maybe if he lived things wouldn't go right. maybe that's why he said he could be a hero if he sacrificed himself hiro made it pretty clear that you can't change the past, only shape the future. i guess after this season ends we'll have a few more clues regarding the shows space/time mythology. i'm just taking some guesses here.