They did intend for it to happen; Brian Cranston was told to take that huge pizza and throw it on the roof, at first he didn't think about how he'd do it, the script said throw the pizza on the roof, he was then handed the biggest pizza they could find in Albuquerque and wondered " How am I going to get this up on the roof? The producers specifically wanted the pizza thrown on the roof, have it separate from the box and land exactly where it does in the show. The Fluke was that Brian done it in the first take, he's even so shocked he almost breaks character and looks at the box with a momentary facial expression change, so brief you'd miss it if you weren't looking.

Here's the interview where they talk about it: Breaking Bad Pizza on Roof Scene - Pizza of Destiny