Red John spares Lisbon at the end of the first episode of the 6th season. But he doesn't just let her go, he puts his mark on her. It's as though he is marking his territory. He is sending Jane a message that she is his.
We all know which one of the seven suspects like Lisbon. Ray Haffner. He had previously proposed lisbon a job offer and when Lisbon rejected it in the name of work, he was quite irritated and accused her of liking Jane. Clearly, he has a crush on her.
In the second episode of 6th season, he visits her and while leaving says
"I like you terasa, I really do . And one of these days, you and me, will have our time."
And in the episode where he warns Lisbon and Van pelt, he was definitely warning them about the BA and did not think telling them to back off before Red John gets them was necessary. Red John doesn't like the BA as he killed Brett Partridge. There is absolutely no reason for Red John to be a member of BA. Sure, he could control them and get what he want done (cleaning his mess). IHim being a member of BA just doesn't seem right.
But of course, if we take Ray haffner as the Red John, some things still don't make sense. Like why would McAllister tell jane that he was Red John?Did Red John blackmail him? I don't see Red John telling McAllister " If you don't get killed by Jane, I will kill you" .
But, well, Ray Haffner still makes more sense than McAllister.