Yeah, the issue of "protectorate" being associated with Omega Pyre is one of those things you're not going to be able to avoid. The new Commonwealth faction had to go for a synonym to avoid being just another callback to OP.
Naming the faction after a single planet isn't a terrible idea, if the planet is far enough away from existing major factions. As proven by the recent Sith rebellion, rebellions do work, so as long as it isn't picked up as a capital world by an emerging new faction, you can feasibly still grab it as you go major, provided you're willing to do the work.
Anyway. I have no valuable input. Factions aren't really my area of expertise.