this will kill the pure PvP aspect... unless you can cook up some reasonable monetary rewards for winning PvP battles.

How about the bounty system back, for starters?

Cunjo: That's the idea, that fighting will at some point have financial rewards, but be costly, too, and therefore risky but potentially profitable.

"Scaling repair cost based on the value of scrap would be interesting. At present though, I don't plan to tie it to any outside factors until the dynamic economy is present, and I can start to attach things to more relevant, real-world supplies (like, say, the cost of component parts which are actually used to "create" the ship in the universe)." Sounds perfect.

As for discounts, the faction idea sounds good. Maybe the extreme discount also factors in faction standing with your faction's enemy. That way, if you fight a lot of Itani, you get more Serco discount for your service. Bulk discounts are also a good idea. Even better, insurance policies. You could pay a certain amount per week/month to have unlimited repairs up to a certain amount. Or you can pay a weekly/monthly amount to get a certain percentage discount on all repairs. These would of course only apply at participating stations.