It depends on how you want it to be cooked when it's done-chewy, crispy etc.
Do you put it under or on top of cheese?
When I've used pancetta, I make sure it's very thin and put it on top of the cheese, and it works fine. It isn't really crispy though. You could also try par cooking it before you top the pizza if you want it cooked more but not to the extent you have been experiencing.