I don't think there's any need to worry about the other stations. The goal was independence, not to annihiliate all federation supporters (right?)
As long as there are Federal factions in control of some stations, the background simulation will slowly raise their influence in the system when there are no more players actively working to keep CSG's influence near 100%. I don't know for you, but I don't feel like babysitting the system my whole life.
An other reason to do so is that a group of players aiming to put LFE back in control of the system will have a much harder time triggering a new war with no fed-owned stations in the system (they will get much less missions for LFE from the bulletin boards). Stopping now would be like dropping your medicine into the trash bin as soon as you start to feel a bit less sick.
Finally we just cannot let some of our brothers and sisters still live under the boot of the Federation while we selfishly enjoy the sweet taste of freedom a few Ls away from them
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