I think that if you have a positive rep (Liked or better), you should be able to wear their armor without lowering your rep with them.
Not how it works.
Let's say you have bad rep with the Khans, put on Great Khan armor and do every single quest for the Great Khans, making you Idolized. You recieve two different types of rep with them: the basic, general rep that you as a person receive and the one attributed to the you in the suit. The bad rep you had before remains, but NOT as long as you continue wearing your suit of armor. However, the MOMENT you take of that armor, you'll lose your Idolized standing and return to your base rep with them, which would be a combination of both the Idolized good rep you gained while under disguise and the bad rep you had before you ever put the suit on.
Now, if you put a suit back on after removing it, your disguise simply gives you completely neutral rep with them. Kind of annoying for roleplaying purposes, cause if you wanna roleplay as a faction, this often means they'll be less friendly with you when you're actually wearing their uniform.
If you didn't understand that, it's basically this: In the Elder Scrolls: Oblivion, completing quests while disguised as the Gray Fox meant your Gray Fox persona would get the credit for it; not you. New Vegas is the opposite: both you and your persona get the rep. So no need to worry about getting faction rep while under disguise and that rep going to waste: the rep will still go to both the disguised you
and the basic you. There's really no point in wearing NCR gear if they already idolize you, however...You'd action be penalizing yourself.
Another interesting note is that Legion assassins and NCR Rangers will
NOT pursue you while you have faction armor (nor will their respective messengers who bring you benefits). Noticed this with a character I used to play as a Great Khan: my rep with the NCR was bad and I'd gotten the warning quest about how they might try to take me out, but they'd only ever show their faces once I took my Great Khan armor off. A good tip for players who've somehow managed to get Legion assassins on their tail at level 7 or something.