Altering the molecular structure of anything you are going to ingest, if you take the time to reflect about it, sounds retarded. 

Even without knowing the exact implications of it.

I personally avoid even being closed to a switched on microwave, mainly out of conciousness of being ignorant about the risks posed by microwaves.

This guy seems to know a lot about the damage microwaves cause to food.

https://www.youtube.com/watch?v=1cFI2ojj_gE