Sex after rape can be a very difficult thing, and I know too that it can be very challenging for the partner of someone who's been raped or sexually abused. I've been in both situations -- I've been raped, and my partner was sexually abused at a very young age.
My best advice for you is to take things very slowly and gently. If she seems uncomfortable, you might stop what you're doing, and just cuddle with her for a while -- that was something that was very helpful to me when I'd have flashbacks.
Let your partner know that she can stop the sexual activity at any time, for any reason -- you might even want to set up a "safeword" or some sort of non-vocal signal she could use if she wants to stop. My safeword is asparagus, which isn't something I normally mention during sex. And I also have a small motion I do with my hand that indicates to my partner that I need to stop whatever we're doing.
You might also like to check out the topics we have going about sexual abuse and rape in the Support Groups forum -- there's been some excellent advice given in those topics.And some articles that might be helpful:
Dealing With Rape
Advice from an Abuse Survivor
Ready or Not?
First Intercourse 101 Safe, Sound & Sexy ? A Safer Sex How-To
You sound like a really caring and concerned partner, and it's excellent that you're thinking ahead about this. Good luck.
"The only unnatural sexual act is that which you cannot perform."
-- Alfred Kinsey