To disable it. Ex: Board a ship kill/molest the pilot and turn everything off making the ship dead in the water.
Also in reference to the persistent capture-able ships like the Bengal, will we see situations of EvE-like great betrayals of infiltration, where someone controlling some of the systems on these ships can simply turn them off and allow people to board/blow up the ship? That's the story I plan on sticking with though if I ever pass out while controlling a ships shields and the enemy blows it up.