First of all, I highly recommend you get the council of a priest. That's the first and most important thing. Whatever you do, no matter how many replies to this thread you get, you need the council of a good priest. You may also want to contact your diocese for a counselor regarding marriage and even the use of NFP in marriage.
That said, do you know why she doesn't want to continue in the NFP class? What does she not like about the class? Be specific. How many did you attend? Have you considered giving her a manual to read first? There is an online manual that's like 200 pages that goes into detail. Does she understand the general principles or does she think that it's the 'old rhythm method'?
One of the many injustices regarding women's health issues is the lack of education regarding knowledge of NFP. Your wife isn't the first, nor will be the last, who just can't take the side effects of contraception. And the older we get, the less of a practical option it is. NFP is an invaluable tool for women. The "good" part in your senario is that your wife doesn't like contraceptives, so she's going to need to find something that works for her.
If you want my advice, which I'm assuming your post was for various bits of advise that you'll put together and choose what's best for you and her, I'd approach her from a secular standpoint with regards to contraception and try to expose her to as much secular material as possible. I know it's hard because I tried looking for NFP material and kept being directed to Catholic websites. But they are out there.
She needs to understand that NFP is a great tool to understand her physiology and her cycles and won't make her feel as badly as contraceptives.
As for the condoms, if you are opposed to using them on yourself, then don't use them. Period. You can't control what she does, but you can control what you do. You'd have to talk to a priest, but I don't think it's wise to withold from your wife. You put yourself and her at risk for infidelity. Some people here may argue that you're an "accessory" if you participate in the marital embrace if you do, but that's not true. And you can ask a priest and/ an apologist, who will tell you that you are indeed not an accesory. Sex is not a weapon. And she is not Catholic. So telling her you won't have sex with her if she does this or that is doing just that. If she uses a female condom, you can't control that, and you've done your best to voice your objections - therefore you are not sinning. But you can control the wearing of a male condom yourself - so just don't. You can pray for her to cease doing what she is doing. And you can keep working on her in a non-confrontational way. But you can't force her...