It changes the composition of food because it is cooking. You also really shouldn't pasteurize breastmilk by any other means.
All cooking affects the state of the nutrients in food. Some will diminish, others will become more available for absorption, this is why eating a variety of food prepared in a variety of ways is so important.
I once used a scientific papers database to do a search for studies about microwave safety and then read through all of the abstracts and enough of each study to see whether the abstracts matched the actual data (it's sad that the second part was necessary, but researchers sometimes present conclusions that have nothing to do with their data) this included the infamous blood study.
The conclusion I reached was:
To microwave food safely, the best thing to do is stir it well after microwaving.