Witchdoctor was right to embrace something I was yelling about for few months.
Zoners can't be so unified and those that want to break free (lol) should be able to do that. If you feel like Zoners should be separated and weave the politics based on the place they are located in - why don't you do it?
Start a zoner faction, base it on some freeport that's remotely out of the way (basically not Doc's or Mal's havens, or Mudds huge ship parking spot), and start to cooperate with the factions near you.
Want a freeport? Freeport 5. Freeport 1.
Go collaborate with those Xenos, Corsairs and lawful forces or whatever. Start tailoring the politics and make sure they realize you're important. Who cares if there's a council of Zoners, they won't annex you (is annex the word here?) for actually doing a Zoner job. Everyone will know that your opinion counts only in systems your ZoI is (and your ZoI shouldn't extend over 9000)
Basically I was pretty much hypocritical (OMG WTF101) before when I insisted that Zoners are not unified but individual and free, because it's pretty much dumb to demand from people to be free to chose to do what they want. Paradox, right?
So if you feel like Zoners should be different on every freeport, start roleplaying one.