I've had 3 disks broken not by the handling, but by the Wii itself. It's a circular scratch that's pretty noticeable so I'm sure the Wii's doing it. Replacements are costly and it takes a half of my salary to buy a new cd where I'm from so I'd really really like to know, how do you keep your Wii from doing this to your disks?
This person on the Tilted Forum Project forum seemed to get lucky with Nintendo's Customer Service. Try contacting them.
As to trying to prevent the problem, is your Wii mounted in the vertical orientation? According to some websites, placing your Wii horizontally may reduce the scratching of the discs.
I would suggest to contact Nintendo Customer Support, as this seems like a hardware problem with your Wii unit itself.
During normal operation, the Wii should not scratch disks, especially not with a perfect circular. (unlike certain Xbox360 Models)