I notice that professionals tend to always melt chocolate in a basin over steam to prevent burning. I have over time become lazy and melt chocolate in the microwave on defrost as this is SOO easy also doesn't burn it. But I am wondering if the act of microwaving it would interfere with the structure of the chocolate?
If all you're trying to do is melt it, then there's no structure you can mess up. The only harm you can cause is by scorching or burning spots, which might happen if your microwave is uneven and you heat too fast without stirring. But otherwise, the microwave is a great way to melt chocolate. Open it up and give it a stir now and then, be careful not to overheat (sounds like you are), and you'll be fine!
It very well might destroy the structure of the chocolate. Since cocoa butter has a crystalline structure, when it cools it will set differently based on how how it was.
If melt chocolate over water, you're guaranteed (more or less) that none of it will reach a temperature over 212 Fahrenheit. If you melt it in the microwave, due to the nature of the microwave, there might be spots well over the boiling point, and spots that are well under the boiling point. It won't be burned, but when it cools, you might not get the uniform texture that you're guaranteed to get using a double boiler.
See below on how temperature affects chocolate texture: http://en.wikipedia.org/wiki/Chocolate#Tempering
I Agree with Jefromi. However, if you are also talking about the structure of the chocolate crystals, you might want to stir in some well tempered chocolate after you melted the chocolate. In this way you add 'good crystals' to your melted chocolate to improve the crystal structure.