No, it won't change the aroma compared to conventional heating.
Generally, heating does change aroma. But it changes in the same way in conventional heating and in microwave heating (given that you heat to the same internal temperature, which can be very different time and power settings for different types of heating devices).
What microwaves change is texture. That's why the microwave is considered "a horrible thing" among chefs. You can't bake doughs or batters in it, and other things like vegetables can also suffer. Then there is the problem with uneven heating. None of these factors matter with liquids. You can warm milk, wine, whatever, in the microwave, without fearing a taste change.