Unfortunately, scratch removal from glass is pretty darn hard. My windshield was scratched like mad when I picked up the car b/c some moron ran it through an automatic car wash prior to delivery. The dealer actually had to replace the windshield b/c anytime the sun or a streetlight hit it I couldn't see a thing.
As far as getting a scratch out of the glass, there are scratch removal products available that you could try, or check with a local glass shop and see if they can do anything about it. You might get lucky, you might not.