This is a PvEvP game. I would not want it to be any different. Without PvP the game would become deadly dull. And with only PvP the game would have no reward (and become dull).
However, those who engage in PvE more than PvP are the prey to the predator. The predator (usually not having any treasure on board) has little to lose, regardless of the outcome of the engagement. Their prey, on the other hand, has more to lose than the opposition.
What if there were a way to soften the loss of a pirate’s treasure, reputation, and emissary grade after having done several PvE encounters?
Suppose, when you are at an outpost, you could “buy” insurance from an NPC for (1) the treasure you gather, (2) the reputation you would have earned and (3) the emissary grade you had at the time of your ship's demise? This would be optional to purchase and you wouldn’t have to buy all three. Though it shouldn’t be cheap to purchase.
And to collect the insurance you would have to take the “policy” to an outpost after you lost your treasure and/or flag or ship. You could not acquire any new treasure on your way back to the outpost as that would make the policy null and void. Perhaps a timer would start (like a merchant crate timer) and you'd have to report the theft to your insurance agent before it ran out. I don't know!
And what’s more pirate than an insurance salesman and insurance scams?
Anyway, just a suggestion.
