Oh. Oh my. This is a pretty difficult situation for everyone involved.
Let's not sugar-coat it more than we must: you made some profoundly poor decisions in play. For your own benefit, you really need to figure out how that happened. Why did you feel like sexual coercion was a reasonably obstacle to throw in front of the group trying to fulfill their mission? What led you to decide that the gang-rape of a protagonist was a natural thing to introduce into the game? Why did you only realize it was a bad idea after the fact?
However, it's good that you noticed your friend was unhappy and decided to do something about it. That's the foundation of good communication in play. Maybe you can salvage things.
Tools for working it out
So, generally when I've screwed up majorly in an RPG, the most productive thing is to talk about it openly and pick a fix together. Actually once we just went back and replayed a bit of the game ("retconned" it, if you will) because the ending to a session kinda flopped and we decided it'd be cooler to just do it differently, and it resulted in what was probably the best session I've ever played. This kind of editing is pretty rare in RPG culture but it's actually pretty easy.
That said, your friends might want to just put it in the past and not talk about it. That's a perfectly legit way of dealing with something that's actively uncomfortable. So don't try to force the issue (you might mean well, but if you end up creating the impression that you think someone is fragile or incapable of making their own decisions, that can be more off-putting and uncomfortable than the fictional sexual assault itself). Say that you feel like you made a mistake, and that you'd like to talk about X or Y if they're open to it, and leave it at that.
Whatever you do, don't put her on the spot to "forgive" you, and don't make a big show of your contrition and how much you've learned, &c., &c. — that's all just peer-pressure and posturing. Fess up, honestly, and take a hard look at the decisions that brought you there.
I think the best thing you can do is to create the structure that'll keep the group on the same page from here on out. I'd start with techniques like lines and veils or X-card. These'll give you some ways to talk about emotional safety and fun at the table in a clear and communicative but non-judgemental way.
If you'd like more discussion on how to handle boundaries and extreme content, I recommend the short supplement "Safe Hearts" (revised free PDF) by Monsterhearts author Avery Alder.
Fictional rape may hint at other, subtler problems
There are some issues about sexual violence in particular that I want to draw to your attention. Basically, sometimes fictional rape is just the tip of an iceberg of complicated (and probably undesirable) stuff to watch out for, because of the atmosphere that it creates. This isn't necessarily stuff you need to tackle all at once in one big block, but it's good to keep an eye on what you're doing so you can catch yourself if you accidentally slip into some unfortunate tropes about gender and violence in play.
Some examples to consider:
A lot of fiction sorta dances around the issue by threatening characters with rape but always narrowly avoiding it through some contrivance. Playing that can be just as threatening and off-putting as rape.
Is the threat of sexual violence represented as an inherent and inescapable part of being a woman? That can create a really hostile atmosphere, potentially more so than depicting rape itself, because essentially it's saying that being an object and a victim is an inseparable part of being a woman.
Is it only women who face danger in this way? That's actually a sexist trope, embedded deeply into a lot of media because Western culture is generally more comfortable with the idea of women as victims than with the idea of victimized men. (Which doesn't stop men from experiencing sexual violence in reality, in both modern society and the historical past; it just makes it very hard to talk about it coherently.)
Is being raped totally going to define the character going forward? (Hell, is it totally going to define the player's relationship with the group going forward?) Either as the thing that we constantly talk about or the thing that's always hanging over us that we tiptoe around? That's a problematic attitude about women and rape, too.
When you're playing "grim-and-gritty," there's a lot of stuff you should discuss up front. I know torture, egregious violence, ridiculous misogyny, and rape are rather de rigueur in a lot of the inspirational material, but, trust me, they're really not an essential part of creating the mood.
Also ask yourselves whether you actually have something interesting and important you want to do with this stuff: abuse for abuse's sake, as set-dressing and background color, can become grating very quickly.
You've run into a common problem - "Party RPGs with non-Party Characters". Same Page Tool can't fix groups who want different things, and it also can't fix game design that works against it's own game premise. You have a few options:
Class Limiting
"Hey, we're playing X kind of game and these classes/types in this
game don't fit that. Can we just not use them for this game run?"
Games that usually have classes antithetical to their goals usually also have a pretty broad set of class selection, so it's usually not too bad in terms of choice limiting. The other half to deal with is the social contract of your group.
(There's also a subset of gamers out there who deliberately pick the most contrary ideas to what you state the game is about. "Dude, why do you have a Navy Seal character in our game about civilians running from monsters?" Those players are their own problem...)
Building with Limitation in Mind
"Hey, for this kind of game I want to run, these kinds of characters
will need to fit these kinds of situations. Can you spend your
points/pick your skills/build your powers to better fit this?"
This is a relatively good option - you can get stuff like "combat rogues" and such that are better designed for situations rather than splitting off. This depends a bit on the system's ability to allow customization or choices within the class system, and also lets players know up front what they need to consider with a character class build.
Non-Party Play and Strong Pacing
If you can run a game which isn't dependent upon a party structure, all those character classes generally work fine as long as their goals and concepts line up. In these kinds of games you need to be able to cut scenes relatively quickly, not spend a lot of time on wasted scenes and the players need to have good goals to aim for.
That said, usually systems that are more mechanically light work better for this than ones attempting to balance out a lot of abilities, though games like Burning Wheel or Blade of the Iron Throne can work fine for it, mostly because the basic resolution systems allow for quick play and give good goal-building tools in the form of Flag mechanics.
Best Answer
Is she dissatisfied?
Is she upset by this situation? Does she desire greater involvement, or would enjoy more if there were something different about the game? Or does she like her low level of involvement?
There is no way we can answer these questions. They are questions for her. Talk to her, ask her straight out. She may be just fine with things the way they are; her level of involvement may be all she wants. She may prefer to be there for the camaraderie and social interaction, to be a part of the group, more than for the game itself. Or, there may be very different things she wants from the game, which she doesn’t know how to bring up or is too shy/polite to do so. Those are important things to know.
Here, I strongly recommend the Same Page Tool. It’s a great way for groups to get, ahem, on the same page. It will help frame the question of what she wants and what the game is actually providing and how those things differ.
If she’s comfortable: does it negatively affect anyone else?
If she doesn’t want more involvement, is that acceptable to the group? Or does the character who is apparently silent and uninvolved most of the time occasionally piping up cause breaks in immersion?
Again, questions for you and your group. I, myself, for whatever reason just did not get very involved in a game recently. As a group, we decided it was OK for the character to “check out” most of the time, with me only adding in quirky one-liners and tossing out the occasional spell in combat. It fit the character, and the group was OK with it.
In a different game with a different group and as a different character, I may not have gotten away with that. I most likely would have dropped out graciously, since I just wasn’t getting into the game. She may as well, or she may agree to some compromise, to try harder to get involved.
If she does want more, can you reach a compromise that will give her more opportunity to engage?
If there are things she wants from the game that she’s not getting, can you offer more of them without disrupting the game? Or are they incompatible with the game that you and the rest of the group want to play?
Once again, questions for you and your group. Be upfront and honest here; no one wants to waste time on a game that is frustratingly not providing the experience you want, and it won’t improve your game. But if possible, assuming she is a friend/you enjoy her presence in the game, compromise is a good thing. It’s entirely possible that what she wants is easy enough to provide, or a good idea in any case, or something the rest of your wants as well unbeknownst to you.