To leave the BoS faction, you can use the computer located in the fourth level of the Lost Hills bunker, as seen on the picture. But you can't access to this room for now, so the only way to leave the faction is to go to San Francisco, and to use the computer in the underground level of the Brotherhood's bunker in that town. Choose Miscellaneous > Resign in the computer options.If you resigned from the main Lost Hills bunker, the guards will most probably shoot you right after this, so be sure you have nothing to loose.