You see, Red John has made people speak on his behalf.  Of course those people die soon after.  If you steal Red John's "thunder", you will be killed.  Red John could have been Sheriff McCallister; I would believe it.  From the first time Jane met that Sheriff, McCallister had a problem with Jane.  The odd part about it being McCallister is that McCallister saved him; however, if people were watching, and McCallister did nothing, people might get suspicious.  They'd ask why did you just sit there? or How did Jane die, and why are you here?  It is also plausible to assume that Red John setup McCallister to call Jane with that voice, from the beginning.  The "Blake Association" is cops, so they are going to be watched by cops.  Being around police in a police station will make a criminal careful.  Of course, Red John is only human, and he would eventually slip up.  However, he may still be out there.  If he is still out there, he will be aiming for Jane next.  McCallister did not try to kill Jane with a knife.  I would expect red John to try to use a blade of some sort.  Despite the victory for Jane, there is still the Blake association. I have some doubts as well about McCallister naming his organization: "The Blake Association".  However, it would not be traced back by name to police.  Something like Fraternal Order of Police would tip somebody off. 
Despite the victory for Jane, there is still the Blake association.  The people who were obvious members of Red John's secret organization that Jane shot are not suspects anymore.  We are left wondering if the show picks up as usual, without the hunt for Red John. 

We are also left to wonder about the police that are members of the Blake Association. Their supposed leader is dead, but they are all fugitives.  The three star tattoo is a giveaway.  The show picks up two years later, and something brings them back together.   The last words of "RED JOHN": I will tell you who helped me in the CBI.  Was it Gal Bertram?  We already know! 
Could it be that the three tattoo was just a faction.  I could have sworn that Red John would not have gotten so angry at Jane.  McCallister was cool headed, but Bertram was cool headed.  Everybody was calm.  I saw some anger, when Jane called him a sociopath.  I thought Red John would have laughed.  Consider that Red John murdered his wife and daughter; Red John already has retaliated, so he has no need to express anger. I thought that the voice was a setup.  The episode when Jane gets confronted by Red John while being tied up was a total setup.  It could have been real, but it is just so easy to order subordinates to do your dirty work.  Plus, Red JOhn used a gun to kill those film students, and he didn't leave any faces painted in blood. 
Well if McCallister could pretend to be dead, anyone in the organization could pretend to be dead - supposing that McCallister is not the head of the "Blake Association".  I am suggesting any more serial killers from that association be called Blake Association killer(s).  I prefer no more color adjectives for serial killers, unless it is outside the Blake Association.