I THINK RED JOHN IS REALLY ALIVE...
Here is why and i think i have a proof. Let me explain it. But first, sorry about my bad english.
In my opinion, Rj might be Patrick Jane's father, the old man like grand Illuminati master guy Bret Stiles or Brett Partridge.
PJ's father; He knows about really so much things about him, especially his happy times. We know that previous episodes. RJ was killed a happy time from PJ's life.
Bret Stiles; With him secret society in secret place he was going to die, or he show himself like dead. We did not know anything about BS. May be he left society and he is hiding, and if he is RJ he must show yourself in a secret idenity. We will not see BS but we can see RJ.
Brett Partridge; As everyone knows we did not see him face in mortuary. The dead man have 3 points in shoulder, he could not be BP.
AAAAND HERE IS MY PROOF HE WILL COME BACK!
http://i.imgur.com/cvURcXW.png
AFTER THIS SCENE UNDER THE TABLE AND CHAIRS WE CAN SEE A RED CIRCLE AND 5....
