Sometimes I like to drink my raw goat milk warmed up. Will this defeat the purpose of drinking raw milk at all? Will it destroy all of the beneficial properties of the milk?
118 degrees deactivates enzymes with moist heat, and 140 degrees dry. Vitamin denaturing depends on the vitamin.
118 degrees will, to most, feel too hot to comfortably drink, so if you're just warming it slightly the nutrients will remain intact.
As Kewpie said, the mic creates hot spots and thus it's hard to control, but if you keep an eye on it and keep stirring it, that should help minimize any hot spot nutrient degradation.
Other than that, the microwave oven has no unique ability to destroy nutrients just by dint of using microwaves. Microwaves cause water molecules in the food to vibrate, which creates heat, which cooks the food.
Mmm, goat's milk...now I want some. :)
It depends how high you heat it. If you stay under a certain temp (140F, maybe?), it shouldn't destroy any of the milk's properties. However, a microwave isn't easy to control in that regard since it creates spots of very high heat. If you want to drink warm milk, slowly warming it on a stove would definitely be preferable.
If you want it warm away from home, you could set it out at room temp for a couple of hours before drinking. It wouldn't necessarily be warm, but it would take the chill off.