I'm not sure anyone has ever proven that CD-Rs will kill a CDROM2 system. There is quite a bit of anecdotal evidence though.
It does seem certain than a CD-R can leave your laser parked at the edge of the sled travel, which requires that you move the sled by hand. This is sorta "broken", but easily fixed. It also is possbile that when an original CDROM2 system (hammerhead or briefcase) is parked in such a way that it will shatter the already brittle middle drive gear (that would have broken soon anyway), but personally I've never had the sled parking out of range issue with anything but a Duo, so I'm not sure that can even happen.
So in other words, I wouldn't let this sort of thing keep you from playing Meteor Blaster. Besides, if this is an original (black) US or PC Engine Duo that you are talking about, and it hasn't had a full cap replacement yet, its almost certain to break down on its own any day now regardless.