Here was Gilligan's reply in the AMA, with emphasis added:
Yes! We had a long discussion before we shot the pizza on the roof scene about whether or not the pizza should be sliced—because, as all you physicists know, a thrown, sliced pizza would come apart due to centrifugal force or angular momentum (or something like that). And yet, you're right: no self-respecting pizza parlor sells an unsliced pizza. So we figured we needed to explain it (in the "They pass the savings on to you" scene), or else face our audience's righteous wrath!
In Breaking Bad -- as in life -- pizza is serious business.