I know theres lots of gray zones in this game regarding morality, but I thought the NCR are supposed to be generally the good guys...and the only quest where I lose karma when going the NCR route is disabling Mr. House? Is there anyway around this or is this a bug? There is the choice to also kill him, so wouldnt it make sense that just disabling him but keeping him alive is the "neutral/good" karma way to go?

Disabling him is like killing him. It would be more merciful to put a bullet in his head than leaving him unplugged. And I don't think that is the only time you lose karma following NCR route. I don't know if there is a right choice but more what you would be willing to live with.