hi, I have the grey sleepcover on my aura and have had since i got it, and its never scratched the screen. The screen is glass isn't it? The cover feels like a hard cardboard covered in a canvas material. i'd be surprised if the canvas could mark it permanently.
Design wise it isn't the best having that inside flap rest slightly in the screen but actually upon checking mine, it doesn't.
Probably not much help but maybe hunt for a non squashed cover? (of course you shouldn't have to) although they are unnecessarily pricey.