Graves is an autoimmune disease
as you rightly say, and with this condition, the effects of excess hormone are usually multisystemic. When medical treatment fails to manage the symptoms, and depending on the repercussion of the pathology on other organ systems, a decision could be made to remove the thyroid
and continue with subsequent thyroid substitution therapy. Decision to remove thyroid is based on clinical response to treatment.
I am afraid this could be the best option for you at this point in time, based on the clinical appraisal of your physician. I think its a safe procedure and the outcome shall generally be better.
Thanks and hope it helps,