While there's all sorts of arguing about specifics I'm seeing in this part of the thread, it would seem to be the overall solution is, in theory, pretty straightforward.
The Official Factions want a way to deal with (what they see as) stupid independents who are spitting in the face of established RP situations and generally giving them a headache while the Independents want a way to deal with (what they see as) stupid factions who are stifling their ability to RP and causing them all manner of problems.
So it comes down to: how can we deal with people going against the grain because they're ignoring other people and how to deal with the people not willing to work with people logically going in another direction? Instead of arguing about specifics improvements or negatives anyway.