If the official faction that represents the Liberty Rogues decides that they do not want to provide shelter/a base of operation to non-aligned indie pirates operating in Liberty, that's completely justifiable inRP.
It's one thing to be an indie Rogue and be excluded from using Rogue bases because LR- said so, it's entirely another however, if your character or group are of the "Freelance Pirate" variety and are excluded.
It's also likely that they discussed the matter with indie Rogue groups to see what they thought as well. (If they didn't, then I stand corrected, but that's how I would have handled something like that, and I know that the leaders of other official factions out there also communicate with their indies in situations like this.)
As leader of the [LN], I try to keep the lines of communication between [LN] and cooperative, coherent, indie groups, open.
Anyway your idea in general...while it could work for some factions, it would NOT work for factions that represent government bodies within the "Houses", it would create divisions and mucked up politics that make very little sense for groups that represent a government.