I just watched the first Haffner episode again.  I found that their were several elements that made me want to accuse him, but just as many to disregard him.  I found it interesting that he was introduced right after Jane kills Timothy Carter.  He could have requested this assignment with the intention of observing Jane.  This would give him one on one time to see if Jane was convinced he had killed Red John.  Haffner shakes Jane's hand upon introduction.  Haffner doesn't really get into conflicts with Jane, he seems to just observe and take in the chaos that Jane can erupt.  I think Haffner also has the majority of the team (cho, Rigsby, Van Pelt) under him not only because of lack of option, but to see if he can turn any of them to his side.  Haffner has the look and charm that it would take to be Red John.  Theoretically.  if Haffner is working with Bertrum, I think they may have spoken about Jane and came to the conclusion that he knows Red John is not dead and his team is solid.  That is why he was dismissed so quickly.  This is probably a coincidence, but I also found it interesting that Lisbon's arm was injured in the Haffner episode as well as the finale.  Later we also find out that Haffner has ties to Visualize and may have been on the farm.  Haffner also has access to a significant amount of wealth (visualize) and is able to start up a private security firm, which could be a front for the Red John organization.

The major downside to Haffner is his lack of flair.  He is not a show man.