The way it all played out, it looked more like a convenient "excuse" for Nova to do something which she wanted to do anyway...
Exactly this. Nova says that she wants and use the weapon as excuse. Orion tell her two times if she is sure about that and that she can say no, and she continues. Is more obvious when just after the scene Nova asks Orion if it was a good blowjob, that's not the reaction from a violated person, but a horny one. If you have ever done BDSM or rapeplay you knew the difference between no and
no, usually been the second one a security world or, if one of them can't talk, and object in the hand that you can throw away or a movement that tell your partner that he/she needs to stop inmediatly.
I can understand the doubt about the scene, but in the context of the game is obvious if you think about it that is not rape or violation, is just two horny teenagers using Maat as excuse.