The Red John episode with McAllister didn't fit any of the previous 120 episodes. And more importantly, it didn't fit with My Blue Heaven.

Then Heller describes Red John McAllister as a Wizard of Oz character in an interview and Kim Fischer talks about dream worlds on the beach. But Heller also says Red John is dead, several times. He says its past that point. 

So in short, Red John is dead, but the episode with McAllister never happened. There was an encounter with Red John between episode 7 and 9, but I presume its being saved for a 2 part finale.

 Brett Partridge clues cropped up before the episode, during the McAllister episode, and are even cropping up in My Blue Heaven, which is very cruel.

 So, the finale will be a flashback of what happened, and how Red John was actually killed. It will be set between episode 7 and episode 9.

I guess even after the series finale there will be people saying Red John is still alive. No one will be ever satisfied with an answer. McAllister (I think it was a great Red John, with lack of explanations, bad script and etc) is not good enough for some people. If it was Partridge, there will be a lot of people unsatisfied, if it was Kirkland, same thing, and the same thing to the rest of the suspects. 

People can't just accept the fact that the series is moving on, that Red John is dead. I guess even when the series is over there will be people like "Oh, Red John is still alive, its 'that guy', he was the mastermind behind every fuking episode and Heller want us to think he is dead".

This is just like the 5 Stages of Grief:

1 - Denial: People just cant accept McAllister as Red John;
2 - Anger: Fuck you, Bruno Heller! Your show sucks, you suck!;
3 - Bargaining: Well, maybe Red John is still alive, maybe McAllister was just another follower like Timothy Carter;
4 - Depression: (This is when people will realize Red John was indeed DEAD and it was McAllister, problably near the series finale);
5 - Acceptance: Looping on stage 1.
 

'm going to make a prediction here, and I am not sure which one it is
yet, but I am almost certain it is one of these two or at least similar
to one of these two:

1) Jane has been in a coma since the bomb
explosion at his house. It would explain the bizarre circumstances of
the Red John episode... Van Pelt banging her head on the window, the
knife wielding random woman and red johns incredibly unexpected behavior
and that UNBELIEVABLY bad pigeon gag (Seriously, for a show this smart,
what in the HELL was that?) This is further possibly supported by the
reference to Janes life being like a "dream world" in the last episode,
which it very much did seem like at times. I almost fell out of my chair
when I heard the words "dream world" because I had previously thought
that might be the case and they were taunting us with it if it is. I'd
also like to point out another clue for us hardcore fans, though I think
this could probably fit into either theory. In the Red John episode,
the pigeon theme is evident when Jane is feeding the pigeons, presumably
trying to catch one. He says to Lisbon "What beady little eyes birds
have. Tiny dinosaurs, you know?" It doesn't seem like much at the time
but as the episode ends and Jane runs off into the distance, we're meant
to be thinking the episode is over, but the shot pans to the park and
the music turns creepy and there is a man standing in front of a tiny
dinosaur slide with a little girl on it. I know it'll be controversial
to say this with all the people adamant he's dead, but I think we would
all have to admit who this person looks like (BP) This would of course
imply Red John is still alive. It would explain a lot, but I don't know
how likely it is for a show to go down that route for multiple episodes.

2)
Mcallister was not Red John but another surrogate like Timothy Carter
(And a far less convincing one, at that. Mcallister never once
acklowledges he is Red John, he talks about being the head of  the Blake
Association and makes a remark about why Patricks wife and child are
dead -- not why he killed his wife and child. When Patrick calls him Red
John he just looks back at him menacingly and then asks him not to kill
him.) This yet again implies Red John is alive and although the events
we have seen so far have actually taken place, not all is what it seems
and we will be hearing from him again before the end of the season I
suspect. It's possible Red John has the motive of trying to make Jane
like him by having him turn into a serial killer who kills anyone
claiming to be Red John, which he has done twice now. Red John would
show Patrick how much they are alike and beat him mentally while doing
so. This seems much more like the Red John we know than what Mcallister
claimed when he arrived at the church. Red John framing some bureaucrat
for his work and killing Jane at the same time sounds nothing like Red
John who could have done so pretty much at any time over the years but
never has. Additionally, the dubbed voice? I mean really, they just
dubbed over him to do the iconic Red John voice, how unbelievably
unprofessional is that to explain the voice after all this time with a
one line dub over the actor speaking. It's UNREASONABLY unprofessional
and I think Bruno Heller is better than that.

Finally, I add this
bit of information: We're lead to believe that Red John is undone by
his phobia of pigeons which cripples him long enough for Patrick to grab
his concealed weapon. Bruno Heller stated that there was a very
important clue at the end of the first episode of the season but that we
wouldn't understand until later. Many people have now taken that to
mean the presence of the pigeons in the house Lisbon enters was the clue
to Red Johns phobia of birds. I believe this was not at all the clue,
but in fact, the clue is that the presence of a bunch of pigeons the
house Red John was killing Brett Partridge, waiting queitly while Lisbon
looked around, subduing Lisbon, Calmly calling Jane while Painting a
smiley on Lisbons face ACTUALLY EXCLUDES THE PERSON WITH A PHOBIA OF
BIRDS AS BEING RED JOHN. There's no way he could have done all that with
his crippling fear of birds and THAT is the huge clue that Heller was
alluding to. I don't trust a word he's said since then ;)

Another prediction: We know that Van Pelt and Rigsby are leaving the show soon. I predict at least one of them will die soon, probably with the return of Red John.

Also, as a rebuttal to those saying this is a legitimate reboot and Heller is trying to save the show. This is the last season and everyone knows it. Heller has already taken a job to start on a new series and is not trying to prolong this one. This will be the last season and without Red John, what will the series finale be? Some showdown with the FBI? Not a chance.

So I ask you, is Red John alive?

There are a million reasons why macalister is not red john.
My biggest red flag was his fear of dying.
I know that even crazy people crumble in the face of death not red john.

William blake was gnostic. If i could explain gnosticism at its core in one sentence it would be that man is god. And that there isnt a man with a beard in the sky that judges people.
Red john does not believe he wi be judged or go to hell.
Macalister was a pawn.