I've read some where that the development team themselves weren't sure what term to use for "guild" and that they pretty much sticked with guild because they could find any other more fitting.
What I'm thinking about, is not using only one but multiple terms, according to the kind of faction one of this groups is part of. Why not for example call a group of raiders "gang", free wastelanders "group" or "clan" and brotherhood groups a "unit".