I always thought microwaving a baby's bottle was not recommended too, until my son's check up one time and my husband brought a cold bottle. The doctor took it and popped it in the microwave for him.
So I usually use my pre-boiled water from my coffee kettle (its always warm as I drink instant coffee ALL DAY, but if its the middle of the night or I dont have any hot water in kettle, then I will pop it in the mic for 25-30 seconds too.