I agree with Darkflame2006 and rei_vilo that this isn't the real Red John. Bringing in a never-before-seen actor and calling him Red John is too easy and takes away from the drama of the show. Using an unknown "disposable" like this guy is indeed Red John's MO.
"Who can Patrick Jane trust?" is the real central theme of the show. As of the this episode, he trusts the CBI team, finally telling them what he knows. He still doesn't trust LaRoche (what was in the plastic box?), which is probably a wise move.
It could never have been Director Bertram - he was too worried about media and not about what went on.
LaRoche certainly has some baggage, including killing the bomber and responding as he did when Jane was running off to spring the trap ("Busy boy.") My guess is that LaRoche is Red John or another one of his minions. Jane's plan did not account for the possibility that two of the five people on the list (including LaRoche) might be Red John or his puppets.
Jane will get off for the shooting because Bradley Whitford did have a gun with him so his CBI friends can claim self defense for him. Until he realizes that it wasn't Red John, Jane won't care to defend himself. (Maybe Jane will get off because Whitford over-acted so much in the role of Dan Stark last year - another form of self defense. :-) )
The new layer of pain for Jane will be realizing that (a) he didn't really kill Red John and (b) he killed a relatively "innocent" man. This should make for some interesting story lines in the future.