If you are concerned, and your microwave oven is not the cheapest one out there, you probably have a setting for reducing the power. Or at the very least, a defrost option, which also reduces the power. You can melt the oils more slowly with less power and not have to worry about 'boiling' the oil.
But it is soap. What nutrients are going to survive saponification and gelling anyway? And I don't eat soap. I may brush my teeth with it, but I don't swallow!
FYI, all the soap I have made, both HP & CP & CPOP are all much less drying to my skin than any and all store bought soaps I've used along the way. I know it and my DIL & Husband also report the same, so for me that tells me that it doesn't matter how hot the oils get, our soaps are simply better for our skin.