It is difficult to address a kallah we do not know, but we will try and provide some guidelines from experience with different kallot. Hopefully some of the points will be relevant in dealing with your kallah.
1. The Crazy/Impossible issue: It is important to stress that many happily married women (including yourself) keep these halachot and their relationships not only survive but thrive. This does not mean it's easy to keep hilchot niddah. In fact, the reason there are so many boundaries set is that halachah is sensitive to the fact that it is difficult and unnatural for a couple to be apart. Therefore, a stringent set of laws was set to keep us very far away from possible transgression of a very severe law.
It is also important to stress that, with life and experience, keeping hilchot niddah does get easier. A newlywed couple who is fascinated with their newfound physical relationship has more difficulty being apart. Even though the sexual relationship improves with time and experience, it also becomes a more natural and given part of life, as does the period the couple spend apart. Most couples eventually find their own way to deal with the separation period to ease the tension: some try to keep busier with work so that they could be available for spending more time together when not niddah, some spend more social and family time and go out in the evenings to alleviate tension of being home and yearning for each other, etc. She and her husband will devise their own system, and it does get more natural with time.
2. Reasons behind halachot: Though sometimes the reasons given to halachot are true to the nature of halachah, they are not the reason we keep halachah. Halachah is binding because we were commanded by Hashem to keep it. Some kallot appreciate trying to give spiritual reasoning so that the halachot could be more significant to them. Others might find this process problematic, since the reasons given do not always ring true to them, and can sometimes easily be disproved (i.e., why does a pregnant or menopausal woman not need to separate from her husband in order to rekindle their love?). Though ideally it would be nice if everyone related to and loved mitzvot, there is no obligation to relate to mitzvot, only to keep them. It sounds like with this kallah some empathy and understanding might be sufficient. Don't try to get her to keep the mitzvot because they are beautiful, but rather because she will know she is doing the right thing and an important thing. Stress also that when mitzvot are difficult to do, we are rewarded even more for keeping them. She should be patting herself on the back for undertaking the important mitzvah of taharat hamishpachah, but again, she does not need to relate to it or like it.
3. Regarding fear of intimacy, it is important to address this issue with sensitivity and understanding, and stress that many kallot find intimacy intimidating since it is new to them. Detailed explanations often make the surreal idea of intercourse more tangible. We strongly recommend meeting with a therapist on a one time basis before the wedding to address these fears, not because she is necessarily in need of therapy, but because a professional might be easier to talk to about what is really bothering her.
We would also recommend for your kallah a book on hilchot niddah by Dr. Deena R. Zimmerman, the medical supervisor of this site and a yoetzet halacha. It is titled A Lifetime Companion to the Laws of Jewish Family Life. Jerusalem: Urim Publications, 2005. You, and she, may also be interested in our new Kallah Companion, an online course designed to supplement kallah classes. Both are written in a sympathetic tone and address some of the challenges she is dealing with.
We wish you best of luck, and suggest you refer the kallah to the website as well if she would like to ask more specific questions herself.