The main problem with pizza is that due to the oils and ingredients used, and the high amount of carbohydrate and fat, it contains a lot of calories. Popcorn contains fewer calories (at least it should, depending on how much butter and sugar and stuff is dumped on top of it).
However, as long as you aren't eating an enormous amount of calories per day, as a meal pizza is probably healthier. It is more important to eat a balanced diet, representing a variety of different types of food, than it is to eat the fewest calories possible. This is why a diet of nothing but rice, even if you eat the right amount of calories to maintain a healthy weight for the amount of exercise you do, is still bad for you.
If you put meat and veg (or pineapple, if you're one of THOSE people) on your pizza then more food groups will be represented than if you just eat pizza.
Lower calories does not always equal healthier.