Yeah the food molecules were excited by microwaves. But the waves arent stored in the food. They are waves, not particles.
The harm comes from having your body excited by microwaves, radiowaves or any wave that damages your DNA. In other words, stay out the microwave
Lol I think we want to make it that simple, so we close our eyes to the fact that we're dumb for eating food heated up in that manner.
I'm sure they dont tell pregnant women to stay out of the microwave... the tell they ass to stay away from the microwave