Command structures like the military DEPEND ON the protocols of command to be followed religiously. In war they are what helps officers to know that orders given will be followed, they can depend on it. The military, in order to be always prepared for war, must act as if it is at war, all the time, when it comes to the command structure and the protocols of command. A Navy commander who obtains the command of an aircraft carrier has learned that already. One who has lost his command has forgotten it.
I have 24 years as an officer including battalion command. An officer is responsible for succeeding in his assigned mission and preserving the lives of his troops, where possible.
When the chain of command is wrong, it is that officer’s responsibility to succeed in his mission (preserving his ship and keeping it combat ready) and saving his troops. From my perspective, he served his command well.
We look for leaders who can understand and execute their missions and are able to adapt immediately when the enemy contravenes your Operations Plan (as they always do) - not robots.