Yeah, it's quite unclear why the brotherhood suddenly decides that merging man and machine is heresy. Nothing in their background seem to justify, or explain this particular point of view. If anything, given their batallions of bionic augmented soldiers, they should view the Institute as competitors, eventually idiots playing with fire, but not ideological enemies. I'm fine with the new approach, but I can't seem to remember any justification for it. Hell, Zimmer used to flex the institute's muscles before BoS operatives in Fallout 3, even gave one some bionic implants, and nobody even gave a damn.