I just found the BoS bunker in the hidden valley, and used the password to bring them up, but when they ordered me to surrender my equipment I said no, and killed them all. Will this cause problems with the story later on? Because I remember in FO3, the BoS were very important the the plot.

(I still have a save file from before I whooped their sorry asses, so I can still go back if you guys say it's a good idea)

Don't worry, just like in the older Fallout games before the abysmal Knights in Shining armor appeared in Fallout 3, they are a minor faction. Believe it or not, killing them is actually part of the plot in a couple of spots. You just missed an opportunity to interact with a minor and ancient faction, really.

No, they're just another faction in this game, and have no real bearing on the main plot. In fact, one of the mission's you'll get if you side with the NCR is to wipe them out (though you can settle it peacefully if you want).