That's the thing -- Sylar hadn't killed Claire yet in the future. Not until the very end of the episode where Sylar reveals he's been posing as Nathan does he get her power. Remember, Peter was the bomb, not Sylar. Of course, this assumes Sylar wasn't around when the bomb went off (the show seems to insinuate that he was). What I don't get is that they say that Claire wasn't saved at Homecoming, but in the future she's still alive and working as a waitress?