It was apparently cut content. So, in any standpoint you want whether it be economic, practical, political, or whatever. Do you think that Mr. House and the Brotherhood of Steel could EVER co-exist? More importantly, do you think Mr. House is justified for genocide of the Brotherhood?
Personally, I believe the Brotherhood of Steel to be the greatest threat to Mr. House ever. Not including the NCR or the Legion of course. After all, the Brotherhood is all about hoarding tech and think about what Mr. House is. He's essentially living and breathing tech. He may be human but he's just an incredibly powerful, one of a kind robobrain with the Lucky 38 as his own body.
I believe House is justified about killing off the Brotherhood. After all, the Brotherhood is better off not existing. Their rigid codex and quasi-religious military won't make the Mojave sunshine and rainbows.