Now, there are still possibilities that RJ is still out there.

One could be that the one who murdered Jane's family (McAllistar) and the actual RJ are 2 different people (maybe BOTH being part of Blake).

Another one (what I think) is that the episodes that are currently running are indeed 2 years after RJ's death - the real RJ. So what we have seen in the ''Red John'' episode may have been sort of a dream that Jane had caused by the explosion at his house. So later on this season, we might see something that points to that or a full flashback of the REAL encounter.