Yesterday I read something here that made me think... what if the moment when Jane finally discovers who Red John is hasn't been shown to us yet? I mean, he did killed McAllister and this is mentioned by agent Fischer when she talks to Lisbon, but nobody ever really states that this man was indeed Red John, she only says "he stopped the 10-year reign of a mass murderer".
What I'm saying is, Jane kills McAllister, we jump two years forward. We don't really know what happened in that time, maybe killing McAllister was part of Jane's plan to catch Red John, and we will get to see his entire plan and the real Red John in the series finale.
That would be a hell of a trick Bruno Heller put on us. So he would be telling the truth when he says Red John is dead, because he is dead in this moment of the show, two years later, but that doesn't mean he has shown it to us.
Hell, maybe I just refuse to believe that McAllister was Red John, I still believe that there's something better waiting for us, and yes, I'm still part of that crazy group of people who think Partridge is Red John (yeah I know, we're a hopeless case!), and would love to keep sharing theories. Anyway, sorry for my english and thank you for taking the time to read!