I am not sure it is Frye, but I think she will re-emerge at least as one of Red John's disciples, if not actually Red John.  I do NOT think that RJ will end up as one of the seven on the list.  Stiles, Bertram, and Kirkland are too obvious, Haffner, the Sheriff, and the FBI agent are too minor, and Partridge is too disappointing.  I think RJ will end up as someone with whom Jane has developed an emotional connection, and that points to Kristina Frye, who has conveniently remained in the background for a couple of years.

Frye, like RJ, is fascinated with Jane, enjoys the gamesmanship of the relationship, is psychologically sophisticated, manipulative, self-centered, smug, amoral, and well-connected.

Kirkland clearly seems to be in league with RJ, but is too obvious as RJ himself.   It cannot be CBI Ron unless his character is more fully developed in Season 6 - for dramatic reasons, RJ cannot be simply a guy who walked around in the background for 5 years carrying a cup of coffee.  We - and Jane - must have some emotional connection to him in order for this to work as drama.  This is not to say that Ron might not be an RJ mole.

I would also not be surprised if Susan Darcy turned out to be an RJ associate or even RJ.   Even though RJ is repeatedly described as a man, we know from Timothy Carter that Red John may have many surrogates posing as himself, which leaves open the possibility that RJ is a woman.  I would also not be too surprised if Van Pelt - who seems susceptible to psychological manipulation - either becomes or is already a tool of RJ.   She is very idealistic, and such people are prone to be followers of people with grand ideas.  But she is too young to be RJ himself.