Are your tops mirror finish? I got scratches in my tops last time it was in a mechanic's garage also and was concerned that any "fixes" might be worse than the scratches?
Mechanics are like weathermen...nothing is ever their responsibility, or their fault! (No offense to the mechanics on this site, just the ones I've had to deal with in the past!)
There are special polishes and procedures just for this purpose. Many good glass shops can do it for you, or sell you the supplies.