I knew a lady who did the same thing as your wife. She was receiving SSD and worked part-time also. On SSD, you can make up to a certain amount of money each month. If you go over that amount, they stop your SSD and consider you gainfully employed. They tell you the amount you can make, up front.
This lady was caught lying about the amount she was making through employment and they took away her SSD for months. After she had payed back about half of what she owed them, they reinstated her SSD, as she was disabled. However, she still has to pay $300.00/month out of her SSD, which they deduct. She nearly lost everything because of it. This was years after she misrepresented her income.
Yizuman, this is the way SSD works, I am afraid. Once a person misrepresents their income to SSD, they will make them pay it back and they do not have much sympathy for the financial hardships that may put the person in.
Your best bet would be to try and negotiate a monthly amount taken out of her SSD with the SS Dept. I wish you and your wife the best, as chronic illness is draining, physically, mentally and financially. Your devotion to your wife is commendable.