If this forum isn't meant for help questions, I sincerely apoligize.

Anyhow, quick question.
I used to play FO:NV daily, and got my character a very high reputation around the globe. However, during a quest that I need to speak to the Brotherhood's leader, I walked in (forgetting I was wearing NCR gear), and began a self-defense onslaught. I ended up dying a few times (they're not exactly easy when all of your combat points are in unarmed), saving, and quitting. Weeks later (now), I began playing again, only to realize that taking off my armor resulted in neutral forces. I already killed a bunch of them and gained infamy.

So, my question is, how can I advance without killing the entire base of Brothers? Do I just need to wait, or what's the deal?