You may have seen the review in today's Times-Union on Uncle Maddio's Pizza Joint that talked about the disclaimer with its gluten-free pizza, which says you shouldn't eat it if you have celiac disease.
The fact is, just about every pizza place that offers gluten-free pizza has that disclaimer. Basically, it's impossible to guarantee complete safety with a gluten-free pizza unless the restaurant is a completely gluten-free establishment. In a pizza joint, there will always be wheat-based pizza dough flying around somewhere.
My personal opinion is that as long as the restaurant takes all the possible precautions to make your pizza as safe as possible, it's unlikely that your pizza will be contaminated and even if it is, the contamination will likely remain well below the FDA's 20 ppm standard.
Others will disagree with me, but I've never had a problem with gluten-free pizzas in places where I can see the workers making the pizza in front of me.