As people favoring PvE or PvP over the other will always be a thing and excluding either of them is segregating the crowd, here two possible changes that sprung me to mind:
Change to "scuttle ship" or add "pay the ferryman"
Taking by word the message on the Ferry of the Damned, players would be able to sacrifice all the treasure on their boat to call and pay the ferryman to bring them to a random location and to keep all their resources.
This will not deny PvP, but give people the option to refuse it and save them time since they do not have to collect their stuff again. It will require them to have something of value on their boat, so, they have to stay active and to choose to keep something or to sell everything; the first will make them a rewarding target, the second increases their chance to lose their resources besides their treasure.
This will not limit PvP, but prevents people being others' treasure cattle, enabling them to fight back or to move aside.
There could be the limitation that people have to "Pay the Ferryman" before they die and as a whole crew, so either killing the enemy crew fast or stealing the loot unseen is the way to go.
Details to develop are: should there be a minimal value of treasure (loot) on the ship or should they keep all resources or only a part of it as treasure (loot) of every value is on the ship.
Another suggestion is more exotic:
implementing the role of "Davy Jones' servants".
This is not a passive mode, it is an evasive mode, so to speak.
People who join Davy Jones do it to bring him riches beyond imagination, they would get a penalty to all their earnings, collected by his other servants.
Players would be under constant scrutiny of his servants (indication for other players), and are required to be alone (or more?) in a crew, are not allowed to fight others, but are able to sink and sail under water (for a limited time?) untouchable under his protection, as long as they stay on their boat, even sharks and megalodons would not attack them under water on their boat.
But, over the water they are normal targets as everyone else and cannot leave an encounter by sinking under water.
They are of course not invincible and can be killed on land or sunk on water if they pay no attention; their only mean of escaping will be to sail under water for a high price.
And what happens when they mess up? Well, the Kraken will take them down, and they start anew as if they scuttled their ship as it is today.
This would also not prevent PvP, but create another challenge of chase and catch.