From the description it just appears that the OP misperceived one problem existing in game, namely frequent reference to GRI as to Gallic Junkers (like in missions) because the ID and IFF of the latter became the one of the former. Not sure if this is where the idea came from, just a hypothesis.
Still, an intelligence unit comprised of some junkies looks weird. Still, manageable.
My question is why CR is put more hostile than the Enclave? I am flattered as a member of a pro-enclave faction yet still I do not understand this stance.