I was working with House recently and was ordered to take care of the Brotherhood of Steel.. though I think "destroy" was the word he used.

Anywho, this goes for any moment - not just while working with House - but is it possible to initiate the self-destruct sequence to the BOS bunker without everyone becoming hostile and trying to kill me on the way out?

It seems the whole 'blowing up the bunker' option is supposed to be an easier yet more specialized (high science/sneak) way of taking care of the BOS rather than just running in lone or with a companion, guns blazing, trying to wipe out some of the best equipped people in the Mojave.. or rather under it. However, everytime I find myself starting the sequence, everyone in the bunker becomes hostile and the easiest way I've found to deal with it is to simply run as quickly as possible to the exit - constantly jamming stimpacks in my veins with a few paladins possibly making it outside of the bunker to chase me down outside of Hidden Valley until they become overthrown by my aresenal of pulse grenades.

Really though.. if I'm going to have to fight/dodge Gauss Rifle blasts whether I blow the bunker up or just clean the place out.. why is there even an option? Shouldn't there be some sort of "escape pod" type exit strategy or hidden tunnel out of the bunker for when the self-destruct sequence is initiated?

There's not a way to stop them becoming hostile I think. The best way to do it if you have good science is to hack the turret control and set the target to "Brotherhood personnel"

That usually clears most of the first level, however there are no turrets on the second level so you have to do that part yourself. That said, most of the Gauss-wielders are on the first level so it will be significantly easier with them already dead.

You will want good sneak, Silent Running, and possibly a Stealth Boy as well if you are going to try that on that way in, since Paladin Ramos is sitting at the desk nearly 24/7, has guard-level Perception, and is armed and expert with a Tri-Beam Laser.