GC is actually a terrorist faction looking to put a queen in office. One Ruler.. under.. them. Theres really no said ties/breaks I can find aside from what the game putson the faction list. If you wanna live with that great, but I hate the idea that the SP game is deciding things in peoples brains in an online persistant setting. I'm assuming on Discovery they are Pirates from what I was told.
Give them terrorist badges and rights (god you better not), then you can ask they only fly civilian ships. Leave them with Pirate badges and they fall into the organized catagory that is allowed to have a multi-ship fleet using components from all of the world (ala Outcast with the LR boat, etc etc).
I'm all about this hard-coded storybook faction blocking, but certain factions were'nt too fleshed out in the original game and in a persistant online settings you can't assume that diplomacy isnt an option. Pirate and Terrorist are two different thigns ID wise. One is organized and funded through piracy. One is organized and generally not even funded at all. You can't give someone an ID that allows them use a variety of ships, and then ask they not fly those ships because the MOD hasnt made them avaible for it in all fairness and M$ got lazy with modeling. Theres not civilian alternatives for some of a Pirate fleet. If you want to encourage more active and useful factions ,then you arent gunna do it by suggesting everyone uses upgraded Starfleas to defend themselves and rob people in a PIRATE faction.