Right now I'm villified by the Legion for shooting some members. I've noticed that when I put on the NCR armor my rep with the Legion goes to Neutral, and the NCR disappears from my reputation list. I'm not sure if it's a glitch or if it's supposed to happen, but I would think that if I put on NCR armor I would still be villified by the Legion. I haven't tried going back to Cottoonwood Cove to see if they still attack me on sight.