I like the idea.
Historically pirates have always operated under some code beyond, 'kill them all, yarr,' which would only make their life harder and shorter. It more often works like your average land-based muggery, if a bit more disciplined and reasonable. They'll kill you to make a point if you fight them, but if you surrender peacefully, they'll let you live and wont take all of your stuff (after all, if they kill trade in a region, what are they going to make a living off of?)
There are a lot of fanciful misconceptions about piracy to this day that reality couldn't bear out. For example; that gold and riches were the primary aims. They were not (not that they'd turn them down) but what they really tended to go after was food and medical supplies, y'know, the kind of thing that keeps them alive and free. Most would also seperate the (often press-ganged (kidnapped)) crew from the officers and then ask if any wanted to join and live as free (if hunted) men. Though most pirate ships at the time tended to be the result of mutinies by conscripted men. Following which your choices were piracy, starvation or the noose.
Of course there are exceptions, such as the Dread Pirate Blackbeard, but then that's why we remember them, that's why they became legends that capture the imagination.
Naturally I imagine Alex has already thought of this. The game and the pirates are as they are because the game is currently set up to test combat. Given time, I'm sure we may even come to feel a little guilt for the bajillions of what we thought of as brainless pirate mooks we've killed, when they start to talk to us and beg us for table scraps, after they ran away from their evil hegemony masters. z: )
