When asked to destroy the BoS for the NCR, it actually takes my NCR reputation down?! I am idolized by the NCR right now. I go into the Bunker, steal the keycards, and set off the self-destruct sequence. Everything is fine, however, as soon as I get to the second level, I have to kill BoS people and each one killed seems to bring my NCR rep down. Any advice?

Nevermind, I just left my companions outside. It turns out that a stealthboy was necessary for me to get out without fighting anyone. If I had a companion, they attacked on sight. So I recommend leaving any companions topside for this quest.