Tl;Wr Create punishment options that kill the fun of being a troll, by costing them time, and removing them from their trollish activities
My punishment ideas:
Tie them to the mast! (Captain pop up) Force a player to stand against the mast of the ship for a length of time, along with a pop up explaining the reason (2 mins?).
Bound and gag them! Same as tie to mast, with VoIP disabled, for the profane.
Keelhaul them! (Captain pop up plus crew vote) Player is slowly dragged along the keel from bow to stern, with VoIP disabled, dying at he end for an added measure. (3-5 mins??)
Walk the plank! (Same rules as kicking player) An alternative to kicking a player, that adds a long animation to waste a troll's time
STOP READING HERE IF YOU DON'T WANT TO BE BORED
Why this will help eliminate trolls Most trolls aren't "professional trolls". Nobody spends $20 on a game with the intention of ruining everyone else's fun. Most trolls are just bored. Maybe they have been playing a little too long, or the game isn't as fun for them as they expected. Creating a bit of chaos is fun for a bored person who is "doing it for the lols". If you waste their time, and make them even more bored, they'll go troll someplace else.
Why voting is important for higher penalties 2 mins against the mast isn't a big deal, and everyone will be able to see them being penalized. A captain abusing this bit of power will be quickly mutinied. Once you take away their VoIP, and hide them under the keel, no one will notice. The voting makes their crime, and the decision to punish them public. It also forces team unity. If the crew disagrees with the captain, they can say so without having to mutiny an otherwise capable captain
This can be used for non trolls This can create "teaching moments" for a player who isn't following the ship's rules. Perhaps a team is a system of stations, and a newbie isn't learning his/her place, and is running around accidentally creating havoc. Or, maybe someone is being especially annoying on VoIP (I was stuck playing for half an hour with one player screaming "mutiny the captain!!" every time we were hit by a volley). Gagging them for a bit will calm them down.
Why this is important from the devs point of view. This game relies heavily on teamwork and leadership. As it comes closer to release, the game will become more competitive. Sending saboteurs will become an effective strategy, as captains realize that they can take turns trolling the opposing team, racking up wins for each other. When a practiced team has a perfectly timed broadside ruined by one player running down the line, you'll see how this unwanted behavior can be useful to a couple of jerks. An internal form of punishment will be important to keep mods and devs from becoming inundated with reported players and trolls as the game population grows.
Tl;dr Create a simple system of historically fun forms of punishment to eliminate trolls and unwanted strategic behavior.