It's a PvP game, no doubt about it. That being said, I do have a few ideas that lean in that direction. For one, Having a matchmaking system that tends to put Single players with other singles would be nice, I think. It doesn't do anything about aggressive PvP'ers, but then, why should it? Refer to my first sentence. What it would do is make it a bit more pleasant for people who just want to play alone, or don't have any friends online and don't want to play with randos (to which I say, "Just try it, it's not that bad,"). But hey, sometimes you just want to play alone. Nothing wrong with that. You'll still be in a PvP game, with a distinct possibility of getting murdered, stolen from, or sunk, but at least you won't get your ship rekt every time you run into someone else because it's a 1-man Sloop against a 4-man Galleon.
Something that I very much would like to see is additional Ship Customization options for those darned "Aggressive PvP'ers - people who've killed many players in man-to-man and sunk many a vessel in ship-to-ship combat. That'll give Players who don't want to get involved a fight a chance to look at a ship and say, "You know, that guy's gonna wreck my ship, I should not go that way," while at the same time, giving other PvP'ers the knowledge that there's an experienced fighter on the server with them: a sort of, "That guy's got a kill-count on him. I wanna fight him," kind of thing. This will also present a new opportunity for the PvP'ers to ally up, or for PvE Players to hire them out for protection.
At the same time, the devs could implement a system of Ship/Personal Customization options for those who have a really low kill count, but a lot of voyages completed: the PvE players, the merchants, the bounty hunters. So then, those players get the option to display a flag that basically says, "Hey, man I don't wanna fight, I'm cool, I'm just tryna go about my business, please leave me alone." Other PvE players have the benefit of knowing they don't have to worry (for now), and the PvP'ers can say to themselves, "I bet that guy has good loot. I'm gonna wreck his world." As with the PvP customization options, this will give PvE Players an opportunity to form alliances with each other, and PvP'ers will know that they've either got an easy target or someone who needs a bodyguard.
Of course, both options present a distinct opportunity for deceit, sabotage and betrayal. Good thing it's a PvP pirate game, huh? Fact of the matter is, it's a PvP Game about Pirates. Yes, getting my character murdered, ship sunk, and loot stolen is annoying, and yes it's a d****e move to do that to someone. It's a ____in' pirate game, that's the point. If you don't like it, either do it back, get better at defending yourself, or go play something else. I bought and play this game to make friends, make enemies, find booty, fight some fights and generally have a good time.
I understand your concerns, but frankly, I think you misunderstood the core concept of this game. About pirates. Whose sole mission in life is to steal people's stuff and kill anyone who gets in their way.