Okay, I can't believe I'm writing this -- and I'm going to further develop this theory later on but for now just want to say that THERESA90's post got me thinking: she's makes some great points.  [though I have never loved the split personality plot -- Jane could be something like "A Beautiful Mind" schizophrenic/sociopath -- a brilliant man who shuts himself off from his killer side]  

For all these years, RJ knows about Jane but Jane doesn't know about RJ -- but RJ wants "acceptance" by Jane -- meaning that RJ side of Jane has been trying to emerge for years, but Jane doesn't want to see this side of himself.  So, Jane had to kill RJ -- but since it's himself that he can't see -- he had to "project" this onto someone.  McAllister

So, I listened to conversation Jane had with McAllister right before Malibu. McAllister, in Napa, was about to shoot a deer from his car until his phone rings.  Jane is calling him.

"This is Sheriff McAllister"
"Sheriff, [it's] Patrick Jane."
"Hello Patrick, how are things?"
"Good, good. I'm calling because I had a question"
"Shoot"
"Last month when I was in Napa, you said you were at my disposal"
"Yes, I remember"
"Did you mean what you said?"
"I like to think I'm a man of my word"
"Oh, I don't doubt it"
"But can I count on you for your help. Can I count on you?"
"Of course"
"Thursday night at 8 o'clock, I'll need your help.
"Then you got it."
"Thank you. I'll let you know where to be day of"
"Patrick, this is about Red John, isn't it?" 

Whole conversation is a double entendre...and it's all to McAllister's detriment!  Here we are suspecting McAllister and he's the damn prey!!

1)  McAllister was a "man of his word"  -- Jane knew he could use him if he needed to
2)  Jane asked for "his help" and McAllister helped Jane to set the stage in his Malibu house
3)  McAllister said "Shoot" and Jane shot him
4)  Jane tells McAllister you're "at my disposal" -- Disposal means=to get rid of something. Jane disposed of him

YES, Jane could COUNT ON McAllister, indeed!  Jane was counting on McAllister to be RJ for him!!  And it worked.  Jane won, for the moment.  

The McAllister in the church wasn't the same as the McAllister in the car: one was under the influence of Jane's hypnosis -- of JANE TELLING HIM THAT HE IS RED JOHN.  McAllister played a part.  He was a STOOL PIGEON!  Pigeon is a great clue...but not because Jane used McAllister's bird fear against him -- BUT because everyone on the LIST was in danger of being RJ's "stool pigeons"