It depends on the size of the tank. If it is a small tank then you are probably out of luck. If it is a larger tank you may be able to polish it out with some jeweller's rouge (sp?). You can pick it up at your local glass shop. You will need a drill and some kind of buffer to apply the rouge to. It comes as a very fine powder. Wet the area and then apply a small amount of the powder. Use the drill to buff the scratch out. The glass will heat up almost immediately and you will have to keep misting it with water to keep it cool. Keep applying a small amount of rouge until the scratch is removed.
It will slightly distort the glass as it basically melts the first layers of the glass. If it is thin glass then make sure and support the other side of the glass as you will need to apply a fair amount of pressure.
The other thing to note is that this will only work on scratches that are barely detectable to the touch. Deep scratches can be reduced but they will not be completely removed.
I am not sure of the chemical makeup of the rouge but it smells like clay and I do not think that it will be harmful to a tank. Just make sure you thoroughly rinse out the tank.