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! 