I would put my money on Bertram as RJ. 

In the episode "Strawberries & Cream part 2" Bertram had been given the room number above O'Laughlin in the hotel, where Hightower was purported to be staying. That is the room that the assassin first enters.  Why would RJ's assassin bring tools to repel to the room below rather than simply enter the correct room? One possibility is that both RJ and RJ's accomplice (O'Laughlin) had been given different room numbers and RJ did not know which was correct. Thus, the assassin needed to bring tools to access both rooms.

In the same episode, Bertram (inadvertently?) gives Jane the idea that the assassin's rope is an important clue by stating that Jane appears to be at the end of his "rope." This is what changes Jane's opinion that Rj's accomplice is O'Laughlin, not Bertram.

Finally, Bertram can use his position at CBI to facilitate the hire of his associates within the agency and arrange for the elimination or transfer/escape of those in  CBI custody who might know his identity.