Ok, as someone with thyroid issues myself, let me see if I can offer some help.
First of all, I want to commend you on being so concerned about your wife's health. I've got the HA in the family, and my husband thinks I'm crazy half the time. It would be nice to be shown a little more concern!
Anyway, I regularly see an endocrinologist to deal with my hashimoto's hypothyroidism, and when talking with him, he reassured me that yes, thyroid cancer is rare. However, if you do end up getting it (or in this case, your wife), that is THE cancer to get, because the survival rate is almost 98%. I have a girlfriend that had a goiter on her thyroid along with nodules and the doctor recommended that her thyroid be removed. She had the surgery, and when it went to pathology, it turns out she did, in fact, have thyroid cancer at the ripe old age of 24. She needed no further treatment. The surgery was enough. No chemo, no radiation, nothing. I do want to say that she's been on meds ever since to replace her thyroid, and is actually currently 38 weeks pregnant with her first child.
I want to do the best I can to reassure you that because he doctor's have been keeping such a close eye on her thyroid, the chances are pretty low that she would have thyroid cancer. Think of it this way - if there was the slightest worry regarding the doctors, do you think they'd risk their medical license for not recommending surgery? No way. If the doctors even suspected cancer in the slightest bit, they'd be removing that thyroid ASAP - they don't want the risk of being sued.
Also, my endo mentioned to me during this conversation that thyroid cancer is always very slooooooow growing. It's almost always caught when it's localized just to the thyroid and hasn't spread. And with the doctors eyeing her thyroid, there's no way they'd miss that. There's no way it would have a chance to spread because she's being monitored so closely.
I don't know if statistics make you feel better, but if they do, here is a website regarding statistics in thyroid cancer. I want to warn you though, if statistics DO NOT usually make you feel better, please do not click on the link. I don't want you to see the numbers and think "well, there's one in a million chance, so my wife MUST be that one." http://seer.cancer.gov/statfacts/html/thyro.html
I hope I've helped!