The fact that McAllister appeared so briefly as a seemingly insignificant one-shot character in the series' second episode, and is now suddenly an important figure at the forefront of the Red John investigation is a pretty solid indicator that he is likely Red John.

His strangely aggressive behavior with Grace Van Pelt outside the winery, during that second episode (Red Hair and Silver Tape) is never explained, and even though I've always found that scene suspicious, I was inclined to dismiss it as a plot device to give Lisbon a plausible reason to leave the motel room she and Jane are staking out. Jane is then forced to confront the husband and wife killing team alone, which makes for a better climax when Lisbon then kicks the door in and is forced to kill them both. I'm beginning to think that my initial gut reaction to that bizarre behavior McAllister exhibited was bang on, and I should have listened to my intuition from the get go. If Sherriff Thomas McAllister isn't Red John, they're definitely buddies.