Do we know if Red John was only a member of Visualize when he was young in the 80s or if he was in the cult even as a 'grown up'? 
I don't know why but I always thought Red John had some kind of respect for Bret Stiles especially if he was still in Visualize and that he would never kill his 'guru'. But McAllister didn't even care about killing him for a second. Maybe I'm too sentimental because in my mind even if RJ is a psycho, he wouldn't kill the person who helped him so much in the past that easily.:D 

So either: Red John is not McAllister and/or Bret Stiles is alive, or: he was McAllister, Bret Stiles is dead and this is just one of the million things that we didn't get an explanation for..I hope it's the first option. I want Bret Stiles to be alive so much!:)