I read harem manga and even I agree that what they did was messed up. And they even acknowledged it themselves. But, I understand why they did it.
And that's why the MC needs to put his foot down and let them know that if they put him in conflict with anyone again. Then they go their separate ways.
1. They are super useful for the story later on as bodyguards
2. They know his secret so betrayal is not the best idea
3.If he did nothing, millions would die from the invasion.
4. He a good person. I would have helped in the exact same way.
MC needs to grow a spine and kick them out of the ship. From getting him involved in a war that has nothing to do with him, and now putting him at odds with a prince when this is all over he needs to kick them to the curb and focus on his goal on getting his luxury liner. and never deal with annoying females.