That just has to be about one of the hardest things to order or to do.
It is hard. I'll share some of my experience.
I spent many hours on guard duty while in the Army. The first several sessions caused me to go through a lot of "what ifs" concerning the situation. Having never killed anyone before I thought through the moral dilemma of having to take lives in order to save my life or the lives of my fellow soldiers.
Eventually I KNEW exactly what I planned to do and had no doubt whatever that I would be able to carry out the plan. I was fully prepared to kill any number of people to prevent the breach of our site security. After that, guard duty became just hours of boredom.
Commanding a ship or part of a ship would entail the same type of process. I expect that the crew had already thought through the necessity of saving the ship if some incident created a breach below the water line. There wouldn't be time during the incident to weigh the moral arguments. If water is rushing into the ship, you close the watertight doors.
This.