From the article, we have opponents cite things like the chemical changes in the food, which seems less important once one reads studies about the chemical changes that occur when any food is cooked, for instance this article points out that slow cooking at lower temperatures is safer than faster cooking at higher temperatures... which of course one could take as saying that no cooking is probably even safer, given the proponents of diets like "The Zone", one could even say that the way we evolved to eat was diets of raw food.
Of course, this begs the question of those of us raised on microwaved food (not to be confused with microwave meals, my mom's a fine cook and a master of the microwave)... is that not irradiation of one type? And haven't we been playing the GMO game to one extent or another for centuries in terms of our food supply, albeit at a much slower pace?
Would today's hippy descendents at Public Citizen be aghast at the concept of pasteurization of milk? We have people pointing to the complicated drug interaction problems with fen-phen as a reason not to trust things that have been tested safe... one could wish that this healthy dose of skepticism was better directed.
I for one would be thrilled by the "unnatural" effect of keeping my food free of E. Coli and other pathogens. Not that I wouldn't mind if my meat wasn't quite so industrialized, hell I'd even love it if my meat was automatically generated out of the relevant molecules a la Star Trek, but American's like their beef... and they like their food cheap.