Long time lurker here. Unlikely to change, just wanted to chip in.
I'm seeing a lot of talk here of removing the ability to be friendly with the pirate faction from the game.
Please don't.
I can definitely understand why it'd make the game so much easier to handle events by just having them as permanent bad guys that exist to be slaughtered and give experience/supplies/be combat fodder, but I've always appreciated the tone it sets by having pirates be a mix of outlaws, (noble?) rebels, bloodthirsty psychopaths, and people just trying to survive. Being able to get on their good side (typically at the expense of your reputation with the major factions) is something I've always enjoyed, even if it's typically quite difficult (which suits me fine).
The pirate playstyle represents a huge change to how you play the game and see things, and I've always enjoyed it as being very difficult, but also very rewarding. No other faction you join presents nearly as much of a change as the pirates do (both thematic and gameplay wise) - though I acknowledge exactly what makes me enjoy it so much also makes it so frustrating to integrate as an option, being so different from the standard approach of 90%+ of players.
While I understand that trying to account for the player being friendly to pirates might make a lot of events more difficult, please consider an alternative solution that would allow for the player to remain friendly with pirates, just because it's something I really enjoy about the game that adds a lot of depth to it (even though it's giving you a huge headache in terms of complexity).
Alternatives? Maybe having event pirates be 'marauders' or 'raiders' something and always hostile as a separate faction (to represent those who will never co-operate with you, the worst side of the pirate faction who have no qualms in dealing with a rival), or maybe just nullifying reputation loss for fighting pirates in self defense (hey, you're just proving you're a badass, right?).
I don't really have any perfect solutions (both of those would still take a fair chunk of work, I'm well aware). Still, I wanted to let you know some people really do appreciate that you can play pirate, and I wanted to make my (entirely selfish) request of keeping that feature intact, because I really enjoy it.
Besides, I'd hate to lose that wonderful pirate friendly market theme. It's amazing how the song transitions from being hostile, suspicious and threatening when you're hostile to the pirates, then going to noble and hopeful when you're friendly with a few small changes. Really gives the theme of a desperate rebellion, or just trying to stay alive.