There is this eyeglass scratch remover on the market sold on tv (stuff usually sux), that supposedly fills the scratch with a resin and makes it dissapear. Supposedly works with plastic as well. Might be the way to go.
EDIT: Stuff sucks, doesn't work not one positive review on Amazon. I would check my local eye glass store for something that does work. Maybe there is something that works.
END EDIT
I have never removed the plastic cover since I got mine for that reason. My gp32 anti glare coating came right off, so I learned my lesson. If I ever have to take it off, I'll get one of the screen protectors for pda's and put it on.