I am, sadly, pretty lax when someone on my ship doesn't listen to me. I don't know if they can't hear me, think I'm talking to someone else, think that whatever they're doing is better than my orders, or are really trolling. Usually, I can figure out a way to make up for their incompetence, but if they really are trolling, I'll troll them back. It's not hard to turn the ship so that they can't shoot the gun they want to shoot, or going to a hiding spot and having a deck party while I bad mouth them in a playful, not-serious way or remain completely silent (works incredibly well) . They eventually get bored when they see that they're unable to make me mad, so they'll either leave mid-match, or they'll leave the next match when I continue to not fly the ship.
This hasn't happened often, and when it does, the enemy and allied captains are sympathetic enough to deal with my issues.
Other than putting up with it or trolling back, there currently is nothing we, as players, can do. I agree that we should have some way of getting rid of these players, but such a large scale segregation would cause more harm than good. I still think the best way to deal with this is giving power to the players. MUSE says we can't kick, so we need some other option that could be used in-game to dissuade players from playing independently and encourage teamwork. Kicking a player off of the guns, maybe a button that could mute them for the entire ship, or even a way to replace them with an AI, forcing them to watch out something.
I figure a Captain abusing a 'kick' function or similar power would be a metaphorical death wish. There are two other witnesses on a ship that could report a captain for abusing his power.