In the Podcast for "Exodus, Part 2" Ron Moore said a couple of times that they had planned to kill Jammer in this episode, but decided to keep him around. When they decided to keep him, they also toyed with the idea of showing him crawl out from underneath bodies after the explosion. Severed limbs, etc. I doubt he's a Cylon.
That said, another post said that although there are 12 Cylon models, the 7 we've seen so far have some sort of mental block when it comes to the other 5 models. They don't even think to wonder what they look like. My bet is that one of our Cylon friends is going to break through that programming... D'Anna? Caprica? Sharon?
And what's the deal with this "Baltar can project just like a Cylon" thing?