Maat does simply kill the other guy when she sees he doesn't want to play the game. From her perspective the MC and Nova were still playing the game they agreed to play by coming to her server. She doesn't know that Nova's gun is a weapon of Atlas, she thinks that the MC and Nova are just using the "random gun that Nova has" as an excuse to keep playing along.
Just like the "murder" in the Roman server, or the medieval fantasy server. You join a server to take part in the game in the way that server is set up.
Your hypothetical example doesn't fit what we see because... (in no particular order)
1. This isn't the real world, or even set in the in-game real world, it is set in the in-game game of Eternum. A game everyone involved in has agreed to the risks of playing. Nova and Alex even bring up that the game can cause paralysis and blindness if you are disconnected improperly. It's one of the risks of play, just like cancer is a risk involved in smoking. You don't get to cry foul anymore if you get lung cancer from smoking for years. There was a time when servers (like cigarette companies) tried to hide what might happen there and use loophole to commit crimes (see point 4) but that seems to have been changed and now servers have to be upfront about what content they allow, and you are expected to participate in. From what we've heard there are even non-combat servers, I imagine committing virtual murder there gets you in trouble, while virtual killing someone in a combat server is just par for the course. The same with virtual sex.
2. Even in the real world, if you go to a free use rape-play party and there is a safe word given, or a way out (which in the context of the scene the MC and Nova have, they can just let Maat reset their level), or you see what is happening and stay then yes you are consenting to play along. You have said you enjoy being "forced" to do something "you don't want to" because you actually want to and are just pretending. The hypothetical falls short because that girl can just leave. If she can't leave, then it isn't a "sex party" that everyone came to voluntarily, it's lying, kidnapping, and raping. If she came voluntarily, saw that the guy was a fat old man, and she wasn't into it, she could have just left. And no, what she says matter, if there is a safe word and she says it and it doesn't end then yes, it is rape. If there was no safe word, then she was dumb for going, but yes then it would be rape in that context, but again, this hypothetical is so far removed from the scene as to be nonsensically.
3. The scene we are talking about happened in the context of a virtual world where death doesn't matter and is not permanent and no one shows up anywhere they don't want to be. If you go to a server where the hypothetical rule is, "You have to fuck the owner of the server when you arrive or get shot in the head." Yes, you consented to have sex or get killed. If I travel to England then I'm consenting to drive on that wrong side of the road. I'm consenting to not be allowed to carry my firearm in public. I'm consenting to all the laws of that land. If there were a free use country in this world then I wouldn't visit it, but if you did then yes you would be consenting to having sex acts done to you regardless of really wanting it at that moment. In the same way, if you join a server you are consenting to abide by the rules of that server, so if it is a free use server, well either don't go, or be ready to spread those legs and cheeks.
4. Nova and Alex even talked about people being excommunicated for trying to use server rules to take advantage of people (children specifically), perhaps with fine print, or by sharing access without disclosing the way the server operates. Luna even brings up cults being allowed broad range of privileges to do what they want, so it is likely that a sex cult could operate freely in Eternum so long as they were open about the rules of coming to their server. We see that in servers where rape is not allowed the Pretorians show up quickly. So, it stands to reason that since they didn't arrive when the MC and Nova were in trouble that either neither of their bodies (which the game reads all the vitals of, remember Luna talked about it being able to pull you out in case of fire or health issues) were not reacting with real distress, or Maat's server is set up to allow dubious consent in sex acts thus the Pretorians didn't come.
5. The other guy is the perfect argument against the example you gave. He didn't want to play Maat's game, so she reset his level. The MC could have closed his eyes and not watched; Nova could have refused to strip down. Would it have sucked to have their level reset, yes, but they could have come back the very next day with Luna, Dalia, Annie, Alex, and Calypso and gotten Nova's weapon back.
Nova and the MC would not have actually died if they had just said, "No Maat, we aren't playing your game, just kill us." They could have even told her the truth, "We found the Weapon of Atlas Calypso, it allows you to access servers outside of the normal ways. We were teleported here by accident and didn't agree to this, we don't want to be a part of this. We did come here for your treasure, and we didn't follow your clues." From what we've seen of her she probably would have wanted to hear the full story and if she had believed them, she probably would have felt like shit for what she had done since they didn't agree to it. She isn't a bad person; she's just playing the game in a way she thinks everyone there is down for. And when she saw that one guy wasn't down for it, she reset his level, no big deal in the long run. She might have kept the gun for herself then, it's a powerful piece of loot, but it's doubtful she would have kept pushing them or even killed them then. She probably would have just looted them and sent them away.
I'm a trauma councilor and deal with victims of actual rape often. I have one patient that can't even watch scenes in games or movies that have rape in them without having a panic attack. I and others have to vet all the media she consumes. She's getting better, she can watch some small things now if she knows about it going in, but it's still hard for her. So, I take the topic of rape seriously. I also take the topic of falsely labeling things as rape when they aren't seriously too. I don't want to get into the real-world applications of the view that consent can be withdrawn after the act is done. I've seen it destroy the lives of real students in my life (both male and female). Maat didn't commit a rape, she didn't even commit sexual assault, she committed sexual harassment at worst. She didn't know the leverage she had over them, she didn't know they weren't there by choice. Maat likes to turn the tables on people who have come to rob her, to reset her level and take her things, and she enjoys the danger in luring people in and then overcoming them. She assumed that everyone in the room was into that too, and when she realized the other guy wasn't she sent him home to the real world with a virtual bullet to the virtual brainpan. No one in the room was "forced" to do anything, there were not in real danger. They could have opted out at any moment and gone home to the real world.
I've gone on long enough, I thought about putting more but I'm ready to move on, so I'll just end this here. If anyone wants to add more, I may respond to direct comments or question but if not, that's cool too, we can all just move on from this. The ball is in everyone else's hands.
Edit: I want to be clear that, nothing I wrote was meant to be a personal attack or anything, it's just my thoughts and ideas. I hope nothing I said came across overly aggressive or anything. As I've said before, I'm a long-winded blowhard,
