I haven't yet had the chance to act this scene out, but I have thought a bit as to how it would work so the sub could still have the fear factor in the experience.
"how could this scene possibly work when you already know that it's not real and that you are actually very close to the person"
In reality, rape is a very devastating thing to the victim. It is comforting to have the knowledge in the back of the sub's mind that the 'rape' is not real.
I think to play out this scene you would have to play a lot with the senses. First, of course, you would talk with your partner about the fantasy. Find out what each other's turn ons and turn offs are, what you each expect from the scene. After it is settled and you both know what it is that the other is wanting, you tell her (or him) that you plan to fulfill the fantasy, but that there will be no warning as to when it happens and just leave it at that for a while. Give them time to let the thoughts slip away, so that they are not expecting it when it does come.
If you live together, you need to be away from the home before you begin the scene. Maybe you'll say you've been called in to work, or you're having a night out with friends. Choose something that would be believeable in your situation. If you are not living together, that just makes this part easier. To play on her senses, you will need to smell different. If she is accustomed to your scent, she will find it comforting rather than bringing out the fear aspect. Shower with different shampoo and soap and wear a different cologne. If you're hairy, maybe shave or trim some of your body hair, give her a different feel. Wear clothes that have an unfamiliar feel or that are not washed with your normal detergent. Basically, make yourself smell and feel like a stranger. When you are ready, sneak in the house (night would probably be best), be ready with a blindfold so that she doesn't have a chance to see you. Scruff your voice up a bit, it would probably help a bit with the scene. And the procede to play it out as you had discussed.
Her mind will be overrun with the sensory aspect. You'll feel and smell like a stranger, and that should be foremost in her mind. But the knowledge that you have planned this will be tucked away in the back of her mind. Just far enough so that she can get into the fantasy, but not panic in the way a victim would. If you sense that she is becoming too frightened and truly starting to panic, say something slightly comforting to her that only the two of you would know. Or, of course, ask her if she would like to use her safe word, she'll know then that she is not in any real danger. Most likely though, it won't get to that point.
Now, if this is a fantasy of yours and your partner has suffered any sort of sexual abuse or assult, this may not be for her. Tread lightly and respect her thoughts and feelings on the matter.
Hope this helps a bit and have fun!