Hey mate! I'm 24y/M also and have gone through the exact same thing. My partner is older and we have been together for almost 3 years and we are stronger than ever.
When my partner and I had first met, we took a liking to each other and shared a lot. Our relationship was built on sharing our experiences; mostly the traumatic ones. She kept telling me one particular story (I won't share it because it would be disrespectful to her) that didn't seem to be that bad. Eventually she revealed more and more details about it until she eventually revealed that she had been raped in a horribly brutal way. And what's worse, it was her first time experiencing penetrative sex. She never told anyone for the exact same reason as your partner.
When our relationship was growing to the point of considering whether or not we should be together (I was hesitant because she was such a pure, loving and genuine person while I was very much addicted to self harmful behaviours) we eventually decided it would actually be really good for both of us to be together. We both loved each other and respected each other greatly and had come from extremely traumatic pasts that we had bonded really well over. Basically our relationship became about healing each other. But man, the first time we tried to have sex, it was not what I expected...
I'm not sure if you're aware, or if others in this thread have mentioned, but that hesitance and fear of intimacy she's experiencing might have something to do with vaginal trauma. Basically, the vagina will just tense up and not let anything in, and everything that goes inside hurts her a LOT! This has been something that's still a little bit of an issue to this day. I don't want to reveal too much, so this is proving more difficult to write than I'd imagined. Basically, first time we tried to make love, we couldn't penetrate at all and she didn't let on that she was in pain either (though I could tell). After trying for a while, I was losing my sexual drive and this affected her. She was crying and told me it's ok if I wanted to leave. She thought that our relationship was over and was grieving for it since it was looking so promising. I told her that would be silly of me and that I love her and whatever is going on, we'll work on it. She eventually revealed that she has vaginal trauma (at least I think that's what it's called) and that she hasn't had penetrative sex before or after the incident. Our relationship became about healing the wounds left by that fucking piece of shit that did this to her. It really hit home when you said "if I ever see him in a dark alley somewhere, he'll be eating teeth". I've often fantasised about finding that motherfucker and cutting his fingers off one by one and feeding them to him before I shoot his fucking head off. Pieces of shit like that don't deserve the life they were blessed with. Never had violent thoughts like that in the past, and never had since, but it seems natural. I've spoken to other men who's partners had been raped in the past and their feelings about the rapist, and it all seems to come down to these kinds of barbaric drives.
I digress! So, yeah the vaginal trauma has been something that we have been dealing with to this day. It's gotten to the point where she is enjoying sex very much, and she will have multiple orgasms every time we make love. The only residual aspects are that when we first penetrate whenever we are making love, it hurts just a little bit until she reminds herself it's me and that she's in control.
So down to what to do and what I've learned helps in this situation. First of all, foreplay is VERY important. Someone else mentioned giving her massages. I give my partner massages every day regardless of whether or not we are going to be making love later. Sexual acts without penetration is fantastic too, like oral or mutual masturbation etc. And when you're making love, she has to be in control of the initial penetration. This is purely from my own relationship so obviously it might be different. After that first time, we decided to not put any pressure on the relationship to be sexually active (in terms of penetrative sex) and instead focussed on being comfortable around each other naked and playing with each other. I guess it's about curbing the association to fun and sexy rather than what it had been associated with in the past. Just be natural. Open up to sense what she's feeling and what can be good for her. Honestly, it can be tough for a guy in this situation especially if you're a really sexual individual. I struggled a lot going from being very openly sexual to having to kind of tiptoe around certain areas of conversation so as not to bring up horrible things. In bed, just let her be the one calling the shots for a while. You can't be forward or dominant in bed until you pass this phase.
If it ever seems hopeless, just remember that this random internet stranger has made it work and is now engaged to his partner. There is light at the end of it all, you just have to aid the healing process. I'd recommend encouraging her to go to therapy. We had some luck with her going into a dream-like trance state and me talking her through confronting the rapist and taking his power away (which in her case was represented as the knife he used) and that was hugely beneficial. Nothing else would have been possible without that intense breakthrough. After that, she never had nightmares or insomnia caused by that event ever again. We did it without a therapist, but probably go to a good hypnotherapist or something.
TL;DR Been through same type of experience with my partner. Lots of communication, understanding, nurturing, foreplay for a long time before sex till she says she's ready, and let her be in control of penetration. Definitely be encouraging of therapy. Rape is an incredibly violating experience and to her mind she may think she's been robbed of certain things that are actually still there and in need of nurturing. Help her come back stronger than ever brother; you'll be stronger and wiser for it!