Regarldess of whether the brotherhood is good, evil or neutral (it seems to be that it is neutral and has both good and evil members), wiping out an entire faction of hundreds of people seems pretty evil. And in fact I read on The Vault that you will take a karma loss because some members are in the GECK as being "Good".

It's weird that Obsidian cut out the option to persade House to leave the brotherhood alive.

I'm guessing that like with Cass and the Van Graffs... to work for the Van Graffs you must kill Cass, there's no diplomatic solution. And surprisingly, no option to trick them either. There is a Save Cass mod that lets you lie and pretend she's dead, which seems a common sense solution, but I guess Obsidian wanted siding with the Van Graffs to require you to do an evil act.

Everyone weants the brotherhood dead because the brotherhpood are NOT good guys they are in fact rather evil and have been doing some realy bad things lately.