I think we are in the unfortunate situation that what has been revealed is not that Thomas McAllister is Red John, but that Bruno Heller is not as clever as we thought he was.
I suspect he has fallen into a hole where by he's taken this story too far, and he doesn't know how to clean it up. He's created a tangle of clues, subterfuge, and tricks that he doesn't know how to untangle. The result, for people like us who go over every scene, every trick, every angle, is disappointment.
Episode 6x8 is the biggest let down of the entire series. It isn't so much the choice of who is Red John, it's the execution of the episode. The actor who plays McAllister either wasn't up to the task, or wasn't given enough to work with from the writer. Bradley Whitford (season 3 finale) did a much better job of playing "Red John", and was much more convincing.
Unfortunately we've been hoist by our own petard; we've analysed too much, and expected too much.
