Is there a way to get rid of the Brotherhood wihtout having to slaughter them in For the Republic? The colonel lady mentions a generator, but I can't find it.

I didnt try killing them.. but the generator is on the second level to the left of the leaders office.

You could pickpocket the codes for the reactor and set the place to go nuclear, though I'm sure that might make them all hostile, I don't know as I just wasted everyone on the playthrough where I killed the brotherhood.

The chief scribe, paladin, and the elder have the codes.

Did you do the quest to become friends with them? And is there a way to talk them into leaving?