The ghost ship is a ship that can crew itself. The problem I see is that the heroes always go first in lieutenant encounters. So they can jump onto the ghost ship, fire its cannons at the sea (or at a hero at insane range if you don't think they can target a random empty space),lower the sails, and/or use the captains wheel so it can't escape. This will fatigue all the stations, meaning that the ghost ship can do nothing on its turn. The heroes can repeat this every turn, and can kill the ghost ship with nothing more than their starting coldsteel cannon.

I thought there was an FaQ stating that the heroes cannot man the stations or cannons on the Ghost Ship? I might be wrong though, don't have the pdf downloaded right now.

Not that the Ghost Ship is great either way, with a decently upgraded ship (which they should have in gold) a group of heroes with some nice skills and bonus items (which they should also have in gold) will do far to much damage to the poor thing.