Tbh makes no sense imo. Where do you see rape? Mc even has a crest magic connection of some kind and can see her feelings. Also she can use crest magic and could easily overpower the Mc if she wants to. Also she tells the MC to go on with the game He suggests. Furthermore depending on the route she does have a kink for Mc dominating her and just does not want to admit it. She later does in the after talk scene where its also clear that she is not "broken" and if you saw the other scenes with her the context of their relationship is pretty clear as well as the things she is into. MC even tells her she can say stop and he will. So there's no rape.
Perhaps it was the forced violence of the scene, perhaps it was that none of what happens feel like play. When the sex if finished, nothing is addressed. Kink, BDSM, when it's healthy would address what just happened properly. They's actual aftercare, in both directions. Yes there's a breif conversation afterward while she's leaning against us and says how scared she is of how weak we make her feel, but nothing felt resolved. Yes Nyx could easily have killed us, but that doesn't change the very violent impression of the scene. Yes I saw the conversation with her in the coms room where we offer to get her back home, but that scene felt so divorced from what happen that I found it jarring.
I'd be much more likely to imediatly agree with you, had a similar scene to this happened with the doctor or the mechanic (their names escape me at the moment), because there's been an established flirty and sexually equal power dynamic. It feels healthier and more free.
Mc does not see Lym as Toy he even states that he didn't tell her certain things because he wants to protect her basically the whole scene before the newest scene with nyx is about that that doesn't make sense he even states that Lym is too good for him etc.
He says he wants protect her, and then admits that's not true and not the real reason he's keeping secrets from her.
Everything you're claiming as a defence he did say and then go "well actually no, if I'm honest it's xyz". And his actions prove it, we make Nyx our second in command, officially or not. Then we don't even tell Nym she's being demoted and replaced, and I don't care if keeping that secret is to protect her feelings.
EDITED TO ADD:
I'll give the game another chance and see if things turn out as benevolently as you suggest, but; I still despise being forced to choose between a very violent and aggressive "BDSM" scene and literally becoming Nyx's slave. I don't mind BDSM, it can be fun, that power play scene was far too aggressive for my taste
