Kaz, while I heartily commend you on your excellent explanation earlier in this thread, I feel obliged to point out that elements aren’t polarized. Atoms, strictly speaking, are electrically neutral. Molecules are not necessarily so.
But heat does “damage” them. The main purpose of cooking food is not just to make it warm, or kill bacteria – heating causes all sorts of complex chemical reactions that alter the taste, which can highly dependent on temperature and time; so microwave vs. conventional cooking can have very different effects: the resulting food contains different chemicals. (Hence most microwaved food tastes like crap…and a very few things taste better).