This isn't really a theory, but just some evidence to suggest that there may be  at least an alternate episode/ending of the Red John Episode due to air on Sunday

Simon Baker did an interview on CBS this morning on the 9th of November . The interviewer asks him if he felt nostalgic about finally getting Red John.

He quotes that "Chase is part of the Fun, but you know, we've shot the EPiSODES!!! where I do actually find him/get him"

Here's the Youtube Link: http://www.youtube.com/watch?v=BAH04qP75IM

Go to 0:58 to hear it...

The reason I'mm saying this in hindsight is because this was mentioned prior to the broadcast of "Fire and Brimstone" when there was still a chance more than one episode was about "getting Red John". But we now know that "My Blue Haven" deals with the aftermath of the RJ death and that there is only a single episode where "he claims to get him" . Therefore, due to hindsight if this statement is  true there has to have been more than one Episode/ending filmed.

I know all this might have been a slip up/indirect lie but I think it wasn't said without thinking about the implications later on. 

As for a theory: Kirkland or Haffner...