This theory on Bertram is actually a comment on a post a few minutes ago that said this:

"If Bertram is Red John then how come he allowed his inside man(O'Laughlin) to get killed?  When PJ realized it wasn't Bertram in the mall Bertram could have told O'Laughlin that PJ figured out it was him.  Presumably Bertram would want the inside man killed so that he wont speak just like he did with all the other inside ppl. Bertram couldn't have thought that they would have killed him.  Wouldn't he have warned him to get out of there and then maybe kill him himself?"

My answer to that, which both goes beyond the scope of the original question and is interesting enough that I believe it warrants its own post follows:

To answer your question, you have to look at why Red John wanted Hightower killed. If she is killed, then the killer of Todd Johnson is safe, who we presume is Red John's mole. Ergo, Red John hopes that by killing or kidnapping Hightower, he is ensuring that his mole in the CBI remains secret.

A question that goes along with your questions is: If Bertram is Red John, why does he need O'Loughlin at all? Two potential reasons: O'Loughlin is FBI, not CBI, and Red John does not have, (or it is never stated that he has) a mole in the FBI at this point. He could also use more people working for him in and around the CBI office. The more he is surrounded by loyalists, the less likely it is that he'll be discovered because they can all help cover for him if need be.

However, apparently killing Hightower is more important than preserving O'Loughlin's life. This can't be the case if O'Loughlin is indispensable but it certainly can be the case if Red John has other placed in law enforcement, or if he himself is in law enforcement. 

It gets trickier, however, when we delve into Jane's plan to expose the mole. Assume Bertram is Red John and O'Loughlin works for him, regardless of which one is 'the mole' or killed Todd Johnson. They both hear two different room numbers. Bertram from Jane and O'Loughlin from Rigsby.

Two possibilities: Red John now knows it's a trap or Red John thinks that Rigsby gave the wrong room number. 

If Red John thinks that Rigsby gave the wrong room number, Red John sends the assassin to his room with the gear necessary to rappel down to O'Loughlin's room so the assassin can check both rooms.
If Red John thinks it is a trap, he sends the assassin to his room with the gear necessary to rappel down to O'Loughlin's room. Again, the possibilities cause a split. Jane either realizes that the assassin is going to rappel and suspects O'Loughlin or he misses the clue that Red John arranged for him and believes it to be Bertram. 

If Jane does not catch the clue and assumes Bertram is the mole, Red John knows that the next logical step for Jane is to have Bertram, the mole, lead Jane to Red John. This is what happens at first.
Presumably, the end game is that Patrick looks embarrassed when he accuse Bertram and the evidence shows that the assassin was going to rappel down the hotel. This is supported by the fact that O'Loughlin kills the cops guarding Hightower. He's not going to get away from that crime scene with his cover intact and he knows it. He's going to bring Hightower and her children to Red John or kill them, whatever Red John ordered. Bertram's protection in this situation is that the rope to rappel exists and therefore exonerates him as a suspect.

If Jane recognizes that the assassin is going to rappel down to O'Loughlin's room, Red John understands that O'Loughlin is going to get caught. There's no way he can predict that Grace will invite him along to see Hightower. Red John is okay with this outcome because then it proves that O'Loughlin is the mole, not Bertram, and thus it keeps his cover intact.

Jane goes to Bertram and tells him that HIghtower is ready to surrender, but only to Bertram. Jane realizes this is when Red John will have to make his move, he'll have to kidnap Hightower before she surrenders to Bertram, and Bertram will tip Red John off. Unbeknownst to Jane, Bertram is completely aware of Jane's plan and sets the situation up so that an imposter Red John tails them to the meeting place. This could be to screw with Jane, this could be to see if Jane will kill Red John upon meeting him, or this could be because he's sick of Jane chasing him and wants to end the whole thing. Personally, I think it was kind of a test, both to see what Jane would do and because he enjoys toying with Jane.

What happens? Jane realizes halfway through that O'Loughlin is the real mole and Bertram is in a tricky situation. He is no longer on Jane's radar at all, because Jane screwed up Jane's own plan, and since Red John based his plan off of that, it screwed up Red John's own plan as well. So Bertram leaves. Probably the safest way to play it, in case O'Loughlin calls Bertram as this would tip Jane off. But O'Loughlin doesn't call anybody. Instead, Lisbon calls Timothy Carter with O'Loughlin's phone. Why does O'Loughlin's phone have Timothy Carter's number in it? Your guess is as good as mine, but Bertram's name could have been in there too and, at this point, it wouldn't have aroused any suspicion.
The question is, does Red John win this standoff? In a way. He gets the Timothy Carter/Patrick Jane matchup and realizes that Jane, if he finds him, will kill him. O'Loughlin takes the fall for being the mole which leaves him safe. And Jane is faced with a very interesting dilemna, getting out of jail when he clearly killed somebody. But he doesn't kill Hightower. While this irks him, it's probably an acceptable failure on his part.

That is IF Bertram is Red John. Bertram is my second favorite suspect, based mostly on this exact scene. I personally think Patridge did it, in Malibu, with the knife. I didn't think it was him until he 'died' in 6x01, when it became pretty clear that the show's writers needed to either change Red John from Partridge to somebody else or divert suspicion from Partridge, the real Red John. If they changed Red John to somebody else, they would have kept Partridge alive to divert suspicion from the new Red John. Ergo, they faked his death. This assumes that Partridge was the person they originally intended to be Red John, and I think that evidence is abundantly clear.