Is there a way to effectively clean a Smart Cover without causing damage?
I have found ironicly that using a Microfiber cloth does the job and also cleans the microfiber inside part of the cover. 

I find that when you use it as a stand the inside of the cover collects anything you are standing it on and will the put this dust/debris onto the screen when its closed. 

To add to this looking at the Apple website on Smart covers, the microfiber lining is the same colour as the polyurethane, yet the actual product is grey (just like in the video on the same page).