When I captain a ship I always appoint one member of crew to be 'first mate' so if I get killed or need supplies I can depend on that person to take care of the ship while I am gone.
In your case though, if the captain doesnt appoint a mate, then just doc the ship - it isn't yours to sail and anyone whoi sails her is a thief - not a pirate
In that case, it is always better to doc - I would rather come back to a good ship and sail again then to come back to some some sunken ship.
Thats just IMO
And Skull ^ - TOTALLY AGREE - anyone who comes aboard and just takes the wheel isnt even a thief... just a weasel!!!