I believe that having the PVP risk element is what makes the game so much fun and worthwhile to play, but I think that having a mechanic in the game to help reduce the "victimization" of players could be very beneficial. Many have suggested a bounty system; which IMO would be great. There could be a tracking system for aggressive actions and betrayals. That way the more "peaceful" players would know to try and steer clear of certain individuals. A possible implementation of that could be progressively colorized red-glowing eyes/clothing, progressively colored ship parts, a marked name, sound cues, any type of visible warning, etc. Something COOL. Not only would this warn other players, it could even be a point of pride and notoriety for the aggressive/backstabbing pirate. There could even be an NPC that you need to give treasure to in order to reduce your "aggro rating" (similar to the EVE Online security status system).
To continue my proposal, I'll tell you the story that inspired this post: After much pleading, my brother finally bought the game and started playing with me yesterday. I told him how treacherous the seas can be at times and that backstabbing, attacks, and other nasty things can happen. Today we got through two parts of his TT and cleared a fort without any issue. He had REALLY been enjoying the game. A ship came up to us and they offered an alliance to quickly clear a fort, we were happy to join up and before you know it, we were looting the captains key. Of course, as soon as we open the door the alliance is disbanded and we hear an explosion. Our ship full of planks, food, and cannon balls quickly sinks to the ocean floor. The betraying pirates eventually hunt us down, but not before I hide the stronghold chest and blow the stronghold explosive. It was pretty upsetting, especially for my brother, who was new to the game and very much disliked how easy it was to betray fellow alliance members.
All that to say I don't think he wants to play the game anymore. We are both PVPers by nature (he is high ranked in LoL, I'm a CS:GO fanatic, etc.), but the way in which that situation played out left a very sour taste in our mouth. I do think having something in place as a warning to other players could help mitigate the frustration that more PVE focused players experience, and at the same time give aggressive players a new system to explore.
I don't accept the proposition that "it's a PIRATE game, if you can't handle it then don't play". We all log-in for entertainment and fun experiences. We were having a blast just focusing on PVE for the evening, and we would have happily traded shots with other players if the situation presented itself. Unfortunately, when a game offers the freedom to totally screw over another player without any repercussions, there will be plenty of people lining up to take advantage, and plenty of people who just don't enjoy the game because of it.