I don't get it

The more I think about my thyroid, the more confused I get about modern medicine's approach to treating it.  I am certainly not the type of person who blindly trusts everything my doctor has to tell me, just because they are a doctor.  I respect their opinions because they do have a lot more knowledge and training than I do.  I do, however, know that there are places that our medical system fails its patients.

When I take the time to think about the typical treatment protocol for Graves Disease (that is what I was diagnosed with three years ago), which is an autoimmune thyroid disease, typically a doctor will prescribe antithyroid medication.  In hyperthyroidism caused by Graves Disease, the immune system starts producing antibodies that stimulate the thyroid to produce too much thyroid hormone which leads to the hyperthyroid symptoms.  The antithyroid medication will block the thyroid's ability to create thyroid hormones, which will, over time decrease or eliminate the hyperthyroid symptoms.

In my experience, and from what I have read, usually they will use antithyroid medication for a few years and sometimes it will put the thyroid into 'remission' and you will get back to normal.  If this does not happen, or if the medication is not effective, doctors will usually recommend a treatment of radioactive iodine.  This will basically kill off part of the thyroid so you do not overproduce thyroid hormones anymore.  However, in most cases, and everyone I have talked to that has had it done, radioactive iodine will kill off too much of the thyroid and you will become permanently hypothyroid.  This is what I don't understand.  Why is it better to kill off a portion of the thyroid, leaving a person hypothyroid, than to either keep treating with medication, or try to determine what is causing the autoimmune reaction and try to eliminate that factor?

I realize that no one knows for sure what causes the autoimmune reaction.  I am sure there are genetic factors, but this is why I am going to try going to gluten free.  I have read a few online articles, such as this one or this one, that better explains the reason there could be a connection between autoimmune thyroid disease and gluten sensitivity.  I am hoping to avoid more extreme measures to get my thyroid and the rest of me healthy again.