I'm normally someone who tries to not sweat the small stuff. However, tempered glass can shatter when it has flaws in it. That piece of glass could fail tomorrow, or it might be fine for years, and then one day a vibration or a spray of hot or cold water could shock it and you'll end up with a zillion pieces on the floor. Tempered glass is designed to fracture into small, un-sharp pieces when subject to enough stress, which is why it's required to be used instead of regular glass for bathrooms. It is also stronger than regular glass, but the tempering process introduces internal stresses: scratches, even small ones, can constitute a weak point where a massive fracture propagates from.

I recall seeing one or two threads here on GardenWeb in the recent past about people complaining about tempered glass panels even without obvious defects failing without warning. Give yourself piece of mind and have them replace it.