Whether it's gorilla glass or not, use a screen protector. I have always loved the screen protectors from Screenguardz. Compared to the ones at Best Buy (forget which brand but they were rather stickier feeling), they are extremely smooth and the anti-glare is great in sunlight or other bright environments. Here's their link...
But, if you already have scratches in your touch screen, you might check out the resurfacing compounds from these guys (TDI-LLC Technology). It looks like industrial grade stuff or something of the sort and might work quite well.