I thought perhaps you could have something similar to an ID which is unique to your ship - a pilot for example. It will carry your call sign etc.
What if this fellow was required for launch and could be tractored in by enemies?
You could buy him/her back at the bar or something after x (e.g. 2) hours of being killed by someone (money goes 90% to the killer, 10% commission), or wait a full 4 or more hours for it to reappear in your own hold?
This would thereby carry significance in tractoring in your own faction's pilots as that would mean your allies could reappear more quickly for a 10th of the cost (you can refund the payment that is given to you)