Mal, I never said the house PC factions couldn't be worried about those not one of their members, but that doesn't mean you can restrict them.
To use your example, if there was a Zoner-tagged/IDd ship such as that, and if that happened, and then we got blamed/complained to, we would simply go out stating they are not a member of the AW, acted independently and without the AW's input. They might put a black mark on the Zoners, but that has to be dealt with through diplomacy. Not stating a person can't be part of that NPC faction because you don't want to worry about it. Called freedom, in Freelancer. The game made so you can do exactly this.
[~V~] is a Zoner faction, we don't worry about you. We know if you do something bad, and even if we get blamed for it, we can solve the issue diplomatically, and there is no legal right or real backing for someone to harbor ill-feelings with us about it.