Is it true I have to kill the Brotherhood of Steel to complete For the Republic 2?

I am accepted in Hidden Valley after completing some of their quests, including helping Harding become Elder. But each time I go back to the Dam, Colonl Moore asks if I have found the Brotherhood, yet.

Any ideas? I dont really want to kill the Brotherhood.

http://fallout.wikia.com/wiki/For_the_Republic,_Part_2

If Hardin is the elder and you are following the NCR storyline you have to destroy the brotherhood.