The MC is in the military, so the military culture is going to be a thing, just like the MCs of the various incest harem power trips or NTR cuckold fests have their own culture.There is no way to stop it, although you can skip the event if you don't want to see it.
The MC says it best
"Protocol, tradition - and the fact Kelly would hate me forever - means I simply can't interfere in this.
It is an honor thing, or some kind of military culture thing."
That's what i am talking about, for a game who claims to give us option to shape the mc personality and past and then forces to adhere to this military crap. I don't give a crap about military traditions and respect i would likely shoot chris in the head and get a death sentence that allow this shit to happen to a sibling even a stupid one like kelly.
"This is less about a lesbian molesting someone than an officer trying to impart a lesson, at least from the point of view of Chadwick."
This would be true if chris didn't have multiple sexual harassment cases in her file. I don't really think people would be that lenient if instead of chris it was a random high ranked guy doing it.
"I think that it is a bit of a stretch to say the MC 'doesn't protect their sister', and that they are therefore classified as a cuck, beta, or pussy."
i really hope you don't have a sister given that you don't understand the concept of protecting your sister.
It is perfectly fair to dislike Chris or be upset with her. She can, depending on the choices you make, come across as highly controlling, hypocritical, aggressive, possessive in a not at all pleasant way, and murderous. Or, she can come across as badly hurt, lonely, career minded, and respectful of those who do a good job but like to have fun. Or something in between. The harassment claims are there and a valid point, Chris did go into the ATC tower with at least a goal of seducing Kelly. I am sure you have never played a porn game where sexy but somewhat unrealistic behavior has happened.
The last sentence isn't particularly relevant, but it is somewhat illuminating to me. May I suggest you take Chris up on her 'training' in the evening? You might enjoy it, or at least find it educational.