I'm super busy making a raw food dinner for my friends but I just wanted to give you my two cents.
I was just like your wife, SUPER sensitive to anything, getting sick all the time, continuing symptoms even though I was completely gluten free even down to my personal care products, which were also free from gluten cross contamination. I was only working three days a week.
About 2 years ago I went raw. It took me a much longer time to get healthy (maybe 6 moths-1 year) and while I still get stomach aches, I am now working full time and perusing a full time masters degree. It's awesome.
I understand your concern about protein, but I found I did not do to well on nuts as a protein source. I don't know why. Sashimi went over well, (and for some reason goat cheese, especially raw and organic) and I also find that if one or two days a week I eat a normal gluten free meal, I feel better physically and it's better for my sanity.
Mostly I'm fruitarian though, meaning I eat fruit all day and sometimes green smoothies. I'll usually have a very large salad in the evening. Apparently there are people that eat ONLY fruit and thrive without protein deficiencies, but I found that was a little too restrictive for me and I didn't feel quite right. But I think we need less protein than you think. I've been eating mostly fruit for a year and I am fine :-) I do supplement Iron, calcium and D.
I found this out for me by trial and error. I just wanted to write you cause your wife sounds just like I was and I want to help and give her hope! I totally know how it feels :-(
I hope you try raw and figure out how to modify the diet in a way that works for her.