There's some at a few locations, like in the ruins outside Nellis Air Force base or REPCONN Headquarters, both of which are part of Still in the Darkįinally, the quest here is to wipe them out, so if you're strong enough, you just might go ahead and do that.
If you've done (or are in the process of doing) her loyalty quest, though, these paladins might be part of that. There's a pretty good chance that she'll be able to get you into the bunker. There's a couple of reasonably surefire ways of getting into the bunker without violence, though: One important note is that if you tend to wear NCR armor, don't, as the Brotherhood is hostile towards NCR. The problem is hard to pinpoint, since the game's scripts are very complex and there are more than a few bugs.
There's no faction impact for doing ED-E's quest line, so that's not your problem.
