I played on an RP server that allowed PvP, but their system was a very good setup in my opinion. Perhaps something like this could improve the environment:
When a player wants to PvP (outside of Conn), there must first be roleplay, which is already a rule, regardless of what kind or how much. Before ANY shots are fired, both players must agree to the PvP. The "aggressor" (in most cases, the pirate) would initiate a request. The "defender" can then either 1) agree to the PvP, and the fight commences, or 2) deny the PvP request, and immediately leave the area. I'm not completely sure how to totally translate this to Freelancer, but here are my thoughts on how to handle a player who refuses a PvP challenge:
1) If the player is being pirated, they MUST pay what the pirate is demanding to continue (within reason). This should be the case in almost every civilian ship, as most sane freighter captain would never turn his guns on a heavily armed pirate ship over losing his shipment or a meager portion of his credits.
2) In the case that PvP is refused, the player MUST leave the area and not return to the same system for 4 hours, similar to PvP death.