I've seen quite a few plastic windows restored to nearly new. Unless there is something uniquely wrong with your window it should be repairable without having to replace it.

As for preventing it when it is fixed, I'm told you need a soft surface for it to lay on when you have the soft top retracted. There is a shelf that supports the top with the window on the bottom of the stack, and putting something soft there will help keep the window from scratching as quickly.

Keep in mind, this is all coming from a guy with a glass rear window

cdelena is the man to ask.