I was wondering the same thing. what I can add is, the "C", may also be for Clearance. When I did a search for it, I searched rank and interestingly enough the first result came up with Staff Sargent. I think the majestic 12 reference is a bit of a reach but the assassin does demonstrate commando or special services style of hand to hand combat techniques. This is another possibility for the "C".
The 12 could also be a relative number referring to a unit number. We can make an assumption that he is CIA as he also demonstrates an ability to be covert in his appearances with makeup and prosthetics. We can also deduce that he has a background in technical training and possibly electronics. He also works alone which means that he could be rogue element of the government or military specializing in assignations.
One more thing to consider is the remark he made to Frank, when Frank asked "Booth" who betrayed him. Mitch said, "some of the same people" Which may mean, that Mitch may also have been Secret Service. Which may also be an indicator as Mitch had more knowledge than that of the average conspiracy theorist in the Kennedy assassination.
In fact, halfway through the film they identify Mitch as a former CIA operative. A trained assassin and the agent refers to him as a C-12 matter. So, we could assume that C-12 is a code within the CIA for a former agent gone rogue.