Rather than self-destructing the Hidden Valley bunker, I instead sneaked in and killed everybody, finishing the quest for Mr. House.

Actually I had the turrets and ED-E do most of the work for me, so technically I'm still "liked" by the BoS.

Now the part where it gets weird. I went back into the bunker a few days later to pick up some loot. It seems like most of the characters re-spawned.

They also tried to attack me on sight, but the turrets are still hacked so they didn't get far. Odd, since my reputation is still "Liked".

My only explanation is that they've come back as feral ghouls in power armor - which would be pretty freakin' scary now that I think of it.