There are two possibilities regarding Red John. Either it is someone from early on in the show like Sheriff McAllister, or they changed Red John half way into the show. When a show starts it is on a year to year contract and can be cancelled or not renewed at anytime. There is no way that the producers could anticipate they would have 6 years to tell the story and wait until season 5 and introduce a character like Kirkland and have him be Red John. 
They could have started the show in season 1 with Red John being Brett Partridge and decided to change down the road. I would like to think that they had a grand scheme how this would unfold from the beginning and not be flying by the seat of their pants and changing midway through. Bruno Heller has said in interviews that Red John is someone we have seen in the background already, like a Where's Waldo. I believe he said that during Season 4. He also has said that he has had a general idea how the show would play out from the very beginning, so I would think that assuming Partridge is dead it would have to be Sheriff McAllister because everyone else was brought in much later.