No, the only real reason not to heat milk in the microwave is also the best one: because if you do, your baby's momma will kill you. She read all those reports on the internets and she doesn't believe your scientific mumbo-jumbo about upwelling for a minute.
So what's Daddy to do when baby is crying for food and Mommy's out at yoga? Just running hot water from the tap over the bottle takes forever and wastes a lot of water. It takes a while for the water to get hot and then most of the heat is just running down the drain.