This might be a little too simplistic, but taking into account the following, I'd say it's Sheriff Thomas McAllister. I have a second guess - but that comes after.

1. BH says he's been there from the start. Only the Sheriff and Brett Partridge have been there from there start and well, the latter's dead. 

2. 'He is Mar'. Has everyone forgotten this writing on the wall? Call me naive, but was it supposed to write 'He is Macallister (almost dying people might not care about spelling)?' 

3. RJ was 18-30 years old when he worked in the Elliston Farm, the Sheriff seems about just the right age.  

4. Lastly, which has nothing much to do with the show but more the actor, Xander Berkeley would be THE PERFECT candidate to portray Red John. If you watch Nikita (where he played Percy), you'd feel as strongly as well. A psychotic, sadistic yet polished individual with a deep-rooted evil within him. I always pictured Xander Berkeley coming out of the Sheriff outfit and into a sleek suit, revealing himself as RJ.

The only thing that throws me off is the phobia which Sophie Miller mentions. 'Acrophobia', fear of heights. I've replayed that scene many a time and it is very clear she says 'Acrophobia' and not 'Arachnophobia' - which I initially read another theory about this possibility. However, in 6x05, it is revealed to us that Haffner does indeed have Arachnophobia (the scene with him, Lisbon and Van Pelt where he freezes at the sight of a spider). You gotta ask yourself, what the hell does that have to do with anything? At this point in the show, I don't think the writers would write in something like that just for kicks. Was this a huge clue for us, or just to throw us off? If it was a clue, then my second guess would be Haffner. He fits Rosalind's, Father Peter De Bono and Sophie Miller's physical descriptions. 

I have to say, if RJ was Bertram or Smith I would be disappointed. Bertram would be too obvious a choice (oh hai we're gonna make RJ the director of the CBI) and Smith just seems too random a choice.

And admit it, Brett Stiles is too old to be RJ. 

Whoever it is, I definitely am on the edge of my seat for the next few episodes.