Well, I suppose that there would have to be some kind of penalty for breaking faction rules. Although, like several others, I am concerned about the rigid adherence to the "Do what a superior officer says" Rule. For example, on one occasion, I was ordered to retreat by one of the Ltcdrs. I retreated a little way (using thrusters) before returning to the fight and likely saving said Ltcdr's life by aiding in destroying the enemy ship.
We're not all military commanders here. We may have some experience from Freelancer, but I doubt even our highest ranked members make 100% perfect decisions. That's why I feel that some autonomy should be allowed, and the rules should be bendable.