There are very real differences between them, and I agree with you on that.
However, cooking over fire (which I do like to do, preferring to cook over alder because I like the taste) does have harmful effects. I am incompetent to list them, or to usefully contrast them to the harmful effects of microwave ovens (which I agree have harmful effects).
I actually think you could cook with sound frequencies. I have read that ultrasound raises the temperature of babies and that may have harmful effects that have not yet been well studied.
Apparently even using sound to cook with will have harmful effects. Dunno if there's a way to actually cook food that doesn't.
Maybe solar ovens?