If I understand this, a single event (i.e taxing or plain piracy) against a zoner ship will mean the disruption of trade between HUGE factions?
The spending power of the Blood Dragon faction would be vast, the outcasts probably greater and not unlike that of the corsairs. I would imagine the loss of a single ship would count as little to the amounts of profit to be had for the zoners. If it's that uncomfortable to trade in these places, don't go there. If someone constantly pirates zoner vessels, they would be persecuted, not the faction or to a lesser extent even a clan. You can't arrest a country for an individuals crime. That person will be unable to dock at zoner bases, will find most borderworld systems hostile and it will be somewhat uncomfortable for them retreating through them in a damaged ship. Try getting a battered Sabre back from gamma to alpha with half the TBH after you and nowhere to dock and re-equip.
I don't think any ID tag should make you invulnerable to a bit of "taxation". If it happens all the time, change your trade route for a bit. The pirates will have to move to greener fields just like the traders . The idea is to stay one step ahead of em.
A foot note:I know about the passengers to Crete thing. If thats what the corsair clans are saying, don't take em there or take something else. It's not like we traders don't know whats going to happen if we do. We have been warned.