Prof, that's fantastic
The more comfortable you can make her feel, the better. One problem with sex for women is, if you don't have it, you don't want it. The more often I orgasm, the more horny I am. So this is a very good thing and you handled it well, too, proving to her that you are not just a horny bastard but someone who wants to please her, too.
Anyway, the issue at hand...There's a lot of good advice on this board already. All I have to add is the above, plus this: does your girl go to church? If yes, try talking to her minister privately (just you, and get him to promise confidentiality, which as a priest he is required to keep) and find out how he feels about sex within marriage. Explain the situation to him. If he is supportive of your point of view (and he will probably be, unless he is really really medieval), then arrange a meeting between him and your wife. He may be able to do a lot to ease her consience.
Also, make a big point of trying to ALLEVIATE HER STRESS! If she says she is too stressed to make love, then DO THE FRICKEN DISHES! She will appreciate it, and if stress really is hurting her sex drive (and I don't doubt that it is, stress definately kills mine), then helping her out is helping you too.
Finally, keep on being patient and enjoying the cuddles she seems to love. Try injecting a little bit of play into the affection, like tickling, which can liven things up and help to thin the line between passive cuddling and active lovemaking.
Good luck!