I like the fact that you have put thought into this topic which effects a great deal of players if not everyone.
I proposed a different possible solution to help the PVP / PVE balance, a few days ago.
Simply give PVP players something to strive for by mean of rep. This will help both PVP and PVE coexist in the same game.
The idea was then built upon by another player on this forum that would see the ship's title (wooden plank above the captain's quarters... when we finally get to name our ship) floats to the surface after the respective ship is sunk.
Collecting the ship's title would then add to your new "Sea Dog" rep (or whatever they want to call it).
However, the value of the title is a combined PVP stat / percentage of the entire crew which reflects on the ships flags in the way of colour or icon. Hell, even a number.
The associated stat/percentage would determine how much rep is gained if victorious. The flag tells any PVP crew at a glance that the ship they are approaching is or is not worth attacking.
Although even with all of that, I still see issues.
Even without being the aggressive crew who initiates the attack, simply by winning the battle(s) would make you look like a fully fledged PVPer.
I'm sorry to have to admit it, but I really don't see a fool proof way of having both game types coexist without outpost safe havens.
Rare created this monster with half-baked ideas, it's up to them to diffuse it. They say that they are sticking to their original game plan, no safe zones.
Before too long nobody will do quests only to have it all stolen (numbers will drop) then PVPers will have no loot to plunder (even more numbers will drop) and the game will be dead in the water.
[sarcasm]But by all means make scars and other cosmetics a top priority, Rare.[/sarcasm]