Once again I'll say there's no way to limit unofficial factions without limiting the freedom of independent (non-faction) characters. People can fly for whatever NPC faction they like, with whatever other members of that factions they like, and that's not going to change. You seem to be advocating required membership in official factions if you want to play a member of a particular NPC faction, and that just isn't going to happen here. And as long as you can play as an independent member of an NPC faction, you can group up with other members of that NPC faction and decide to fly together.