Did anyobdy notice, that in 06x02 Smith acted like an advisor to Bertram?
Bertram: "So, what does Jane know"?
Smith (angry): "It's your job to find out"!
Bertram? He just nodded!!!

This was not a request, this was an order!!!

The Red John case is a CBI case. Bertram is a Director and Smith just an FBI- Agent. They were sitting in Bertrams office...
Does Smith simply have bad manners? I don't think so. Smith is very likely NOT Red John, but if there's really a kind of RJ cult, Smith's rank is ABOVE Bertram's. And that would rule out Bertram as Red John!