There is a great deal of controversy in the medical literature about oestrogens. On one hand oestrogens are the most effective medicine against hot flashes, and in some hormone related migraines. On the other hand recent studies have implicated them in breast cancer, blood clots, strokes etc. Knowing the risk and benefits of oestrogens, you can make an informed decision for yourself as to whether the benefits in your quality of life are worth the small risk of oestrogens.
There are some other medicines for hot flashes that you may try. Most of them are herbal products. Clonidine is an allopathic medicine that has been reportedly effective for hot flashes and for migraine prevention (very small doses). Discuss the various options with your physician, and make a decision that best suits you. Best of luck!