I think Partridge really is dead.  The reason he is dead is that he was RJ's forensic guy!  He examined every crime scene to remove any evidence that would lead back to Red John.  That's why we see him at every RJ murder scene, and that's why he was the first to be killed.  He knows all the evidence that would link Red John to his murders.  He knew waaaaayyyy too much.  Thus, he was the first to go.

Ultimately this will be RJ's undoing.  Partridge was kind of the brains of the operation.  He kept Red John two steps ahead of everyone.  Now that he's gone, RJ has started being careless and making mistakes, letting Kira Tinsely see his tattoo, not destroying Sophie Miller's voice recorded sessions.  Partridge would have totally figured that out and destroyed the tape.

Regardless of who you think RJ is, Partridge is the forensics guy.  It explains quite a lot.  I still say the Sheriff because he has indicated he's been a hunter most of his life and enjoys killing.  He's an intelligent man, but not the brains of the outfit, so without Partridge, he really shot himself in the foot!