Pretty simple concept here, but the devil's in the details. Basically, Pirates shouldn't work like normal Factions at all, because they aren't a "faction" in the classic sense.
1. Pirates aren't a Faction, they're a bunch of opportunistic people who will kill you if that seems like a good idea.
2. For those purposes, the Pirate Faction is always "hostile", in terms of Player Fleet / Pirate Fleet interactions. If a Pirate Fleet wants to attack, it will.
3. Instead of making friends with the Pirates, the operating assumption is that the Player is always welcome to trade at Pirate bases unless the Player has accepted a Commission. Accepting a Commission means the Player can only dock at Pirate bases if their Transponder is off.
4. Instead of using the "like-->dislike" meter to determine whether Pirates will attack, if given the chance, it should represent your "street cred" within the Faction. It should be hard to earn "street cred"; basically, you'll have to do something difficult and illegal. But if you have enough "street cred", then Pirates who intercept the Player Fleet might choose to leave you alone, because you've gotten a reputation as somebody too dangerous to mess with.
5. Building "street cred" with the Pirates should involve missions that look like Bounties, but are deliberately acts of opportunistic evil; i.e., "there's a fleet carrying necessary medical supplies to Blah World to end the plague there, but Boss Krank bought their insurance policy and wants them to have an 'accident'. $200K".
6. No matter how much "street cred" you have, there's no guarantee that Pirates won't attack you. "Oh, you think you're so tough, don't you? Well, I think me and da boys are gonna have to prove you wrong, amigo...".
7. As an interesting idea, I think that Pirate Bases should be temporary objects, not permanent, Planet-like objects. Each time a Pirate Base is established, it'll last until it has run out of Supplies or has been destroyed by the local Faction(s). Then the Pirate Base disappears and will get replaced in a month or so. Players should be able destroy them, of course, gaining a lot of Faction rep in the process. If a Base gains (X) Supplies as a result of successful raids, then more Pirate Bases should spawn. Potentially, that means that a System could get overrun with Pirates, which sounds like a cool mechanic.
8. There is never a penalty for killing Pirates or their Bases. These give you more "street cred". Getting killed by Pirates, however, loses you "street cred", proportional to the size of the loss. In an Iron Mode game, this would be an interesting mechanic.
9. You lose "street cred" over time, if you're not actively doing things that increase it.
10. Killing Bounties increases "street cred".