Niallo
I'm a private pilot, so I'll skip talking about big iron, but an aircraft commander (frequently called captain) has the authority to override any laws as necessary to protect the aircraft and those on board. So in an emergency, s/he will decide the best course of action. There is an old saying in pilot training 'aviate, navigate, communicate.'
That's a hell of a lot of authority, which is why airlines are very careful who they appoint as commanders.
And it also explains why pilots get paid so much, as they have a commensurate level of responsibility to accompany that authority.
In an emergency, the commander's top skill, analysis and decision making, comes in to play.
For an example, listen to the tapes of Capt Sullenberger.