The following may seem like wishful thinking on my part, but I must say I a strong hunch that the Red John or Blake Association story isn't over yet, for sure. Let me explain my hunch (it's going to be long, so please bear with me)
1. After the Red John episode, I started watching seasons 1-6 all over again. And I realized that there are at least 3 episodes in a every season till date which involve RJ, and RJ playing the cat & mouse game, either to taunt Jane or keep himself "clean" by making some moves against Jane/CBI team. Such episodes are the premier, one mid-season episode and the season finale.
2. Things started making sense when the Blake Association was revealed. Which makes it very likely that RJ did in fact use the BA association to do his bidding (as mentioned in 6.07 by R.Smith).
And on a side note, I really have a feeling suggesting L'aroche is also a BA member. I mean, in season 3 we discover that he has a strange secret. Later, in the finale we in the scene where Gupta (who may also have been BA) was shot by L'aroche and you can see L'aroche acting mysteriously just as Gupta enters the car. Which makes even more sense when we discover that L'aroche did in fact have horrible reason and he somehow managed to keep it in a box and quiet for 9 years or so if I'm correct.
And how do people in the show manage to keep secrets hidden? Answer- with the help of the Blake association. So it would make sense if Laroche comes back in the show and has something to do with the Blake Association.
3. In the mid-season episodes I mentioned before, RJ always has had to make a move to keep his hands "clean". For example- 1.11 with Jared Renfrew, 2.08 with Bosco and his team, 3.09 with Todd Johnson and later his buddy Montiero.
In s4 with Panzer and the morgue attendant/coroner. In s5 with Loreli and maybe the guy Kirkland killed. (supports the infamous twin theory). And now in s6, RJ by making the last move of his game (or was it the last?) and last week with the Ardiles killing (BA if RJ actually died).
4. Not to mention, the season finales have always been RJ playing games with Jane and the next premier episode showing the consequential/continuation of the previous.
So, it would make sense to think that the RJ (or the BA story-line) may not be over, yet. Heller and the team have stated in press-releases prior to the premier of s6 that "RJ will be revealed, i.e caught or killed by the end of 2013.
And besides, The Mentalist, as we all can agree; is all about misdirection and twists.
Hence, wishful thinking or not, we can still expect a major twist from Bruno with something to do with RJ or the BA.
