This is a theory on Red Johns phobia.
I read this short theory on another site but the individual suspected Reede Smith,
i though suspect McAllister instead.
I think that Red John might have a germ or physical contact phobia.

I suspect that Red John doesn't like to come into contact with others
he finds "unclean".This is probably why Lorelei stated
"I'm surprised you didn't become life-long friends the moment you shook hands".
It is probably a big deal when Red John allows someone to 'touch' him and people who are allowed so, tend to become his friends.

Looking back at the episode Wedding In Red, i noticed that McAllister twice avoided contact with Lisbon, first when he passes her to get a closer look
at the hammer on the ladder he actually tucks in his hand into his chest and
at the end when he shakes Patricks hand (before the pidgeon scare)
and immediately brings his hand to his side before Lisbon gets close to him.
This is why i think he always has his hands on his belt, the perception of it
would be that he is just being professional.
This is probably the reason why Lisbon was spared, whatever she came into contact in that house (pigeons for example) kept Red John from killing her eventhough he was wearing gloves.

Just a side note, when Red John was talking to Patrick in the season 6 opener,
he had both his hands on his blade.
I believe this means that he had some kind of communication system
that allowed him to have his hands free,
like the walkie talkie Sheriff McAllister had on him when he sneeked up on Jane.