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Laura, I only had one ovary at the time of my breast cancer because the other had been removed when I had a hysterectomy.  When I developed a cyst on my remaining ovary, my doctor, like yours, suggested just taking it out.  Chemo had already sent me into menopause, so I was glad to have the ovary taken.  Be sure to ask if the doctor if it can be done with a laproscope, an instrument that allows surgery with just a tiny incision.  I was back at work in just a few days after that procedure.  My surgeon did say that sometimes a larger incision is needed.  If you were planning to stay on a hormone suppressant until natural menopause and you need surgery to deal with the cyst, it seems removal has more benefits than risks.