Sorry for late reply. Yea I have legion faction armor on and I still get killed. I am hated with them but not that low

If your level is "hated" with them, this is why.
http://fallout.wikia.com/wiki/Fallout:_New_Vegas_reputations#Faction_reputation
If you look here, "hated" is in red, which means they attack you on sight. You probably shouldn't have killed those dudes, or perhaps been more discrete about it.
It will be very difficult for you to get your rep up with them again, as the bigshots will always see through your armor disguise. It may be possible to pickpocket/kill NCR to get dogtags, and use sneak to talk to the guy who collects them before he goes hostile and thus raise your rep with the legion to the point where you are "unpredictable".
I suggest you kill the legion- you see how they treat their women.