Unless there was a lot of grease or spilled food on the stone I can't say that I have ever heard of a stone turning black in front of my eyes. You might want to heat the stone for about an hour at moderately high temperature (not enough to set off the smoke alarm system) to see if it gets rid of whatever was on the stone. Over time, most pizza stones are prone to some spillage (cheeses, oils, sauce, etc.) and they will turn dark in places but that shouldn't materially affect the baking process in most cases.
If you use a pan, you might consider using a fair amount of oil on the pan before you put the pizza on the pan. If the pan is perforated, rub the oil on with your fingers so that it doesn't drip through the holes. The oil should help give you a crispier crust because of the "frying" effect that oil produces at high oven temperatures. It's not a cardinal sin to use a pan. I use them all the time for certain style pizzas. You just have to learn when and how to use them properly.