Fallout – ny way to follow the Mr. House questline without killing the Brotherhood of Steel

You can only enter the Brotherhood of Steel bunker if you discovered a dead Brotherhood of Steel Paladin and recovered their password, if you have Veronica with you or if you are told to find them by either House or Yes Man. As a last resort you can also pick the very hard lock (100 skill required).

Entering the bunker for the first time always starts the Still in the Dark quest

See the Hidden Valley Bunker for more details.

You could maybe argue that the Followers of the Apocalypse are "Good Guys", but even they refuse to offer assistance to the Strip without some coercion.

As far as the four primary plot paths go though, no, there's no black and white to be had. All four players have redeeming qualities, and they've all done (varying amounts of) extremely questionable, if not outright irredeemable stuff.

In general, the moral choices in FO:NV are not about good or evil. They're about priorities and willingness to pay various prices - which makes for a much more interesting moral landscape.