I microwave Bethanie's, started doing it about 6 months+ I think and still do it. How long depends on how long the milk has been in the fridge for and the amount of milk obviously, so I can't say exactly. We put her cows milk in the microwave for about 45 seconds now and she has about 160ml.. perfect milky temp.
We used to make the milk then heat it up, but if I were you id heat the water then add the powder.
By the way, im sure loads more people use microwave than they're willing to make out. All the bottle warmers leave "hot spots" like a microwave does, but im sure if you shake it and leave it to stand for a minute, it'll be fine. So convenient!