Expanded polystyrene has an extremely low loss tangent and dielectric constant, so I fail to see how microwave heating causes more chemical leaching than hot water.
One might think the water in the soup would moderate the temperature of the other components and keep them from reaching significantly above its own boiling point. Is this intuition not entirely accurate?
The plastic above the water line has no heat sink and can melt if you cook the noodles too long in the microwave. That shouldn't happen when you boil water on the stove and dump it into the cup, even if you cook the water for far too long.