Thanks to the recently resolved writers' strike, Sylar will remain an intergral part of the show in the third season.
Actor Zachary Quinto had origionally been set to drop out of the last half of the second season due to his comitment to playing Spock in the upcoming Star Trek film.

But because of the strike, filming on the Trek movie is complete and Sylar has been written back in.
"Well, we have no plans to say goodbye to Sylar right now," Tim Kring told Sci-Fi wire. "I mean that was yet another silver lining from the strike - Zachary Quinto's available to us in the third volume. That was a huge thing for us to be able to have him back."


I got this information from my Heroes Official Magazine, issue 6.