Is there ANY way to raise your fame with the Legion? I want to do the Et Tumor, Brute? Quest, but I can't get into the Fort without wearing CL faction armor, which means Caesar won't talk to me. I'm a merciful thug with them right now because of the fact that I completed The House... IV and I didn't know that going down the Mr. House route would murder my rep with CL. It also auto-failed the quest where you repair the howitzer at the Fort with the Boomer equipment. I checked the side quests list on the Wiki, and I already completed/failed all the ones listed. The NCR dogtag thing doesn't work, because I have to wear the legion armor to get near the collector guy, and when I give him the dog tags nothing happens since I'm wearing the neutral armor, it doesn't help my actual rep.

Then you're screwed I guess.
Action and consequence.

If on pc you can always use..

player. setreputation F43DD 1 100

In the console, otherwise I don't think any will work for you at the levels needed.

Yep

They told you when you should pick the faction who you are going to work for. <_<

So should I just exterminate the Fort and Cottonwood Cove? I'm a level 30, do I have anything to lose if there's no legion around anymore?

Not really, you could wipe out everyone in the game and still not lose one iota of an ending.