Truthfully any question regarding health tends to be more complex than any 1 or 2 sentence answer you may hear. There has been a great deal of research around this question and the answer is not a simple "yes" or "no".
For example here is a research paper published by The Journal of Food Science that states that chicken cooked in hot water will have lower bacterial counts than chicken microwaved.
http://www3.interscience.wiley.com/journal/119672967/abstract
And another by The Journal of Food Science that states different types of microwave cooking will change the antioxidant activity in Barley.
http://www3.interscience.wiley.com/journal/123208102/abstract
However other studies such as this one by Critical Reviews in Food Science and Nutrition state, "The degree of destruction of vitamins and pigments during microwave processing is not greater than that observed in conventionally heated foods."
http://www.informaworld.com/smpp/content~content=a915467945&db=all
In the end it is not a black or white answer. The statement, "Our bodies don't recognize the nutrients" is probably overstating the issue.
The types of food that get microwaved (pre-made, highly processed foods) are likely worse for you in quality simply due to heavy processing.
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Lastly just know that the education level of people who use the term, "Naturopathic Doctor" varies greatly. Always ask what type of education the person has. There is doctorate degree level Naturopaths. For more information on this level of education see: http://www.naturopathic.org