I think Gellar is already dead and he is the result of Travis's sick mind.
Travis, as Gellar's student, became a fan of the professor/writer and, additionally, the "source of inspiration" to his sick ideas.
Very probably, after having haressed Gellar as an unconditional fan he is, Travis shared his thoughts with the teacher who, obviously would not sponsor his ideas.
He was then, mostly obliged to get rid of Gellar. However, he could not accept to be apart from the one who was his sole inspiration. So, today he's guided by visions of the chosen one (Gellar's phantom, the one who talks with God).
On top of all that, Travis (by using the image of the professor)feels redeemed by his sins and reduces his own culpability level/participation in the murders (he's a believer after all).
He's somewhat like Dex (himself with his inexistent father figure is always validating his misguided actions and choices). Dex builds a "mature" and "reasonable" argument explaining why he needs to get rid of serial/sick killers.
Travis do the same (with his invisible gourou). He must get rid of sinners, thus must prepare the world to the coming apocalypse. He's a minor servant for making good to humanity.
So, I'm looking forward to seeing how Dex will deal w/ this killer. I mean if above exposition is "confirmed", Travis is the only Doomsday killer to be blamed and NOT a simple puppet.
Dexter will be obliged to kill a character who's a bit like himself (guilty but "not guilty?").
About the story itself, hope that Brother Sam survives and that Quinn be less idiot and more professional.