Great theories I must say, I think Bruno Heller might get a lot of script ideas from here.

I think it's Bob Kirkland and not Micheal Kirkland.

From the News article they released we know that it is one of the suspects. Partridge as the producers confirmed he is dead. Now Heller in an interview mocked lost saying it had lose ends, he would not lie about partridge when he makes bold statements like that, which will show him in bad light.

We know Heller will pull a quick one on us. To do that he needs a double twist.
He led us to believe that Bob was a good guy and Micheal to have gone wrong.
Then He killed Bob Kirkland.

I however think that Bob Kirkland is Red John, who sent Micheal to die as bait thus leading us to believe that Micheal might be the baddie, Red John.

Also if you notice when Reede Smith takes Bob/Micheal into the woods to shoot him, he looks surprised, something is off there for sure.

The important thing to notice is that Red John can't be wither Bertram, McAllister or Reede Smith because in the next episode Great Red Dragon, when they Round up Tyger Tyger group, Patrick says "He is one of them" but he already knows that Bertram, McAllister adn Reede Smith are part of Tyger Tyger, then why say he is one of them. So RJ will be concealed with the Tyger Tyger group, and will be revealed in episode 8.

So Bob Kirkland and not Micheal is Red John.