If that's the case, can't they just bomb the ship and be over with it? Maybe don't even bother to unload the cargo, take the fuel and oil out, take the potentially hazardous materials out, take the high value and easily movable items out, destroy the blockage and start a clean up effort with priority of just opening the passage.
Too blunt? Well, that's how we deal with blockages all the time. Probably it is is within the realm of the military tech and operational capabilities, just a matter of cost and time making sense.