Personally, I'd use the pill with caution. The very strong synthetic hormones in the pill are not the same as your natural hormones - in fact, they work against your natural hormones.
Have you experienced other symptoms while on the pill? Hot flashes can be a sign of unbalanced hormones in the body, and since this underlying problem hasn't been addressed, and really can't be until your natural hormones are no longer suppressed by the pill, the hot flashes will probably come back again. This might be why your doctor is recommending you come off of the pill. Ultimately it's your decision, but if you'd like more information on the pill, symptoms, and alternatives, I'd recommend the book "Period Repair Manual" by Lara Briden.
http://www.mayoclinic.org/diseases-conditions/hot-flashes/symptoms-causes/dxc-20319436