All a microwave does is strike the molecules in the substance being heated and make them vibrate faster.
They can harm living cells - but that is not a concern with oil.
Now, if you get the oils too hot, that can cause them to degrade faster. But you are talking about heating the oils to over 200F. And it is not the microwave that causes the damage it is the heat. Same thing can happen if you use a flame or electric stove.
I melt my solid oils in the microwave. Just until I have about 2/3 of it melted. The oil is about 120 F once I stir it to finish melting them. I fail to see how this will harm the oils more than the much higher temperature of gelling will. (I will check the temperature on the next batch of soap I make.)
I'm pretty sure the 'losing nutrients in the microwave' thing has been debunked, and food actually retains most nutrients in the microwave, and roasting/boiling actually does more damage. I think the study was about broccoli...
Either way, I use the microwave for heating oils. Whatever nutrients are in the oils are usually destroyed by the saponification process anyway, so I don't think a quick zap in the microwave will do any additional harm.
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.
I don't melt my oils for soap in the microwave, simply because I soap in a stainless steel pot and use the stove. But I do melt my lip balm and lotion and whipped shea in the microwave, no problem. I do it in short bursts - 2-3 minutes at a time - but that's b/c I don't want the oils to get burned, or to get too hot and boil over.
I too melt my hard oils/butter in the microwave. If I'm using a masterbatched batch I'll disperse my recipe amount and just warm up the whole batch in my microwave. I use 1 gallon buckets or large plastic bowls. Soap being a wash off product, I'm really not concerned with heating my oils/butters. Lye will do more damage to any properties than heating will.