I think that McAllister can't be Red John. There was a lot of birds in lastest season and there was 2 things that dont match:
McAllister said he hates "those things" - he meant bird that attacked him on church tower.
In episode when Lisbon drove to house where Partridge was, there was a room with group of birds inside.
I think that Red John is bird lover (whistling is way to comunicate with those animals), so McAllister was fake, which had to mislead PJ, but I bet it didnt work.
