The author makes it look like she's too nice to be upset at him, but she has to deny him because it's the law. Seriously? She can't just deny the cover up because she's mad at him? Her mind is clear enough that she can reason on the basis of the law, so she could just as easily reason that he will try again if given the chance. Or backstab her on the front line.
Where did you get the impression she's being too nice. That looks more like she's just apathetic about that guy's fate.
She can always report him in the next day, if the others don't got awakened by the noise. About resisting, there's no proof she will just take it and do nothing, she just have more motivation to do it quickly.
Military rules or not, she never have any reason to protect him. But the rule is still a rule.
Although, I'd love to hear if the reaction have to do with her being a man in her past life, so there are mix of things (along with seeing so much dead people) that made her reaction different.
As for the legal implication. Personal opinion, it could just be disciplinary thing: no sex during service, period.
It's not about perpetrator or victim, or morality. And they're not civilian living normal society, at least right now.
The consensual part means she's actively taking part in breaking discipline, so two head flies rather than one.
Or to put it in other words, you and Strela views it in frame of rape situation with the longer term social implication (victim blaming and others).
My opinion here is more focused to the their much smaller community (military). As other comment mentioned, it can sow distrust among the soldiers, and that could mean dead for their corps. Even if it's a consensual relationship, that still brings a lot of implication like some of their members have different priorities (partners first rather than their other comrades), or it can incite other dissatisfaction to soldiers who are already forced to stay away from having romantic or sexual relationship.