Have Graves' Disease,Having Surgery Is It the best Option?

I have Graves' and severe hyperthyroidism, I didn't respond well to the anti thyroid meds. I don't want Radioactive treatment, I am having surgery soon, But isn't Graves an auto immune disease and will the surgery help at all? I know it will with the hyperthyroidism, but what about problems with my immune system? Thanks for any help!