I agree with Trinite, roll with it. My PCs did something similar last week. Second day aboard Mans Promise they decided to do some sneakin around, tried to get into Pluggs cabin for some recon. When they could not get in the Orc barbarian, without consulting the rest of the party, decided to smash through the trap door from the cooks cabin. Well, mayhem ensued and in just a few short rounds, before anyone could come to pluggs defence he almost singled handedly, with a few fantastic rolls, took Pluggs head clean off. With head in hand he very sucessfully intimidated the rest of the crew.
I did manage to let Scourge escape, got plans for him later! The whole thing suprised the hall out of me, but I thought, what the heck, open the sandbox and let them be pirates! Yar Har Har!!!