I think it is definitely Ray Haffner, as he fits the following:

- As per Sophie's description, he is middle-aged, with short hair and a pleasant appearance.
- Also, he is seen whistling as he leaves the hospital room. Even though MacAllister is shown whistling in the end, that's meant to make you forget about the beginning.
- Rosalind said once that Red John's hands were callused. Well, that's exactly what you get when you lift weights!
- His membership in Visualize fits. Brett Stiles obviously knows who RJ is, but wouldn't give up one of his own. I think that's why he helps Jane a bit, because he knows it's wrong, but won't ever give him RJ on a silver platter. The theories about him being Stiles' son intrigue me, too, but I have no real evidence.
- Haffner's affection for Lisbon is one of the reasons why RJ couldn't hurt her in 06x02.
- I also thought the female doctor dropping in to the wrong room, was a bit strange. Like she scoped out if Jane was still in there. Then we see her behind Jane in the hallway when Jane is on the phone. Then Haffner came in to see Lisbon

After 06x02 I'm more convinced than ever.