Microwaving does kill some nutrients, and it doesn't give prana. The best way to heat/cook food is over a fire, but this is not an option for most people.
Second best: using a flame stove top.
Third best: regular electric stove top, and cooking in an oven.
Microwave is last. However, most food is best eaten hot/warm, so it is still better to use a microwave than no option at all.
If you're heating up soup, try to heat it in a saucepan on the stove rather than in the microwave, for example.