You could use the tribunal. Although, I imagine a majority of people would have trouble getting enough hard evidence to make their case for something like this. It wouldn't really affect me much since I'm all geared up for recording/streaming. An hour and a half of HD does recording takes up A LOT of space though, and tribunal matters can take up time and resources to be done properly.
You could also setup up the game to register one player who get permission to board. Set it by whomever does damage first, most damage over a set time, or have people get a random chance for boarding permission if multiple people enter a match at the same time. If someone other then the player with permission boards the ship, they get a pirate flag. I'm not sure how much trouble it would be to program that in though. I guess you could just disable their grapple ability for the claimed ship, but I'd enjoy getting to take some shots at any thief myself.
I'd rather this mechanic not be needed at all. I'd rather the Devs had more time to work on adding content and such. However, some people are greedy, lazy, and others just enjoy trolling. It's pretty obvious that people will continue to do it if something isn't set into the game's code. It wasn't needed before the sales opened up on Steam, but it sure is now.
Also, Admin mentions historical navies several times when he's talking about thievery and rule breaking. He does so quite regularly on the forums when making a point as do many others. I do hope you're not going to jump on everyone that mentions them because the precedent was set on that a long time ago. Eesh, a moderator even says this place is run like the 18th century British Navy. So, I would say that mentioning the British Navy is relevant.