The ship would need to be designed around it, but the battery could be set up in a way to allow it to burn out without affecting the rest of the ship at all, it is not that hard to isolate a battery from the rest of the system.

Although it would be better if the battery is at the bottom of the ship so there would also need to be some sort of air exhaust system for when that happens, hopefully one that prevents the fumes from reaching the passengers at all but I don't think that would be possible without a chimney.