Microwave radiation penetrates all tissue of the human body EXCEPT for eyes and the developing fetus. According to "What to Expect when you're expecting" (not exactly an "alternative" perspective!) she says that developing fetuses are particularly vulnerable to the effects of microwaves.
My mother has metastatic breast cancer. Her oncologist at UCLA (ranks 6th in the nation for breast cancer research) wrote what most consider to be the definitive book on breast cancer (http://www.amazon.com/Dr-Susan-Loves...7329174&sr=8-1
). In this book she talks specifically about the risk of microwave radiation and the development of cancer cells. I really encourage you to check it out at the libraray or at a bookstore if you question the link.
The other issue with microwave radiation is what you put your food on - there have been studies that show cooking food on a plastic plate causes the plastic to leach into the food. Certain plastic are known carcinogen.
I think you have to look at the materials and make up your own mind on the risks / benefits of using a microwave during pregnancy.