It's not a perfect analogy, but it's good enough for me to accept what happened. Humans aren't always rational.
I think for me, the way I see it is... it's a flashback told from the point of view of an officer on the bridge who wasn't privy to the reasons behind the order. Thus having no personal context of what went on behind the scenes, it is what it is. It can be irrational, random, stupid, or whatever, but what matters is that it happened.