As I suggested on the Pirate Update thread, make Pirates able to collect at least individual bounties. Backdoor, Black Bounties make that happen for Pirate ID so at least it would be stated on forum. I don't mean in game bounties like you can do with Freelancers, like "Hey Freelancer I pay you x mil if you engage that xy". But rather the indiviudal bounties, Dark deals, underground pacts and stuff. At least with this, it wouldn't make the pirate ID that bad.
I even imagine that Lawful factions could be sending Highly Encrypted transmissions to certain Pirate Groups to take care of someone or some group which they would pay highly for it. These are like just one time bounties, but secretly hidden. While Freelancers have to register themselfs on the BB, such Black Bounties could be set for Pirates. It ain't "allying with lawful" it's just making the dirty job for money, since pirates are so obsessed for money. : )))
The ones putting the indiviudal bounties can then choose if they want to let a Pirate organization (or just a Pirate) deal with this, or if they don't want to get their name put into dirt, search for Freelancers.