During Season 1, Episode 9, (Flame Red) Patrick told Lisbon "when I catch Red John, I'm gonna cut him open and watch him die slowly like he did my wife and child."
If Sheriff McAllister is Red John, this means:  Patrick didn't really mean it; he forgot; it wasn't practicable; or, he changed his mind.  It may also mean that Sheriff McAllister was not Red John.
Perhaps the two year layover and the FBI gig is an elaborate ruse to make Red John think that Patrick thinks he is dead.  Maybe Patrick will lash out when its least expected and cut someone (later revealed to be Red John) open and watch him/her slowly die.
Perhaps the producers have lost track about what was said and done in the past and are just attempting to keep us entertained while waiting for the series to be cancelled.  If this is the case, the producers will have lost all credibility in my book.