I am not from Laminar Research; just a flight simmer from downunder.
Firstly. to run the disc version of X-Plane you have to have disc 1 in your dvd drive at all times. Unlike X-Plane 10 there is no substitute USB dongle which can be used instead of disc 1.
Having stated the above, if your dvd drive damaged disc 2 then you need to give the drive a detailed thorough clean or alternatively replace the drive altogether. If you dont then you risk damage to disc 1.
The short answer regarding the download of disc 2 contents only is NO. Laminar Research can replace the damaged disc for a small fee. You need to make contact through email@example.com
What you may chose to try is download the digital demo version. When you start X-plane you will be asked if you have a product key. Answer NO. You should then be asked if you have a disc version . Respond YES. Then follow the screen instructions and remember to have disc 1 in the dvd drive at all times. X-Plane should then open and run as the full version including what is supposedly on disc 2 and all other DVDs.