Telling him to wait won't work, you've got to dismiss him entirely I think so he goes back to Novac (or the Lucky 38).
IDK.
I had him wait at the entrance to Cottonwood Cove as soon as I noticed the Legion markers turn red. As soon as I had him wait, they went green again and I had no problem getting in to the Fort. In fact, after coming back, I wiped out everyone there (except the boatman who has some sort of quest attached to him) with a suppressed sniper rifle and as long as I leave Boone outside, I still have no problem going in and out.
Dismissing him for a while should definitely work, though.
Heck, this game reacts in so many different ways for so many different people, I'm starting to think the game A.I. takes on an individual personality or something as it progresses!
LOL!