I think the two reasons people buy frozen pizza is for price and convenience. Compared to fresh from a pizza place, it's a fraction of the cost. Compared to making it yourself, it's a fraction of the work.
I happen to think pizza is a healthful food. It's all about the ingredients. My goal is to make my own dough but I currently buy the fresh dough from Trader Joe's for $1.29. They have three kinds, I get the "almost 100% whole wheat" variety. It usually only lasts one to two days in the fridge so it's best to make it the same day.
My son loves pesto, it's often what we use for the sauce. I like to use half basil and half spinach in my pesto to add more nutrition. If we go tomato based, we use my husband's marinara. I buy shredded mozzarella and that's all the goodness my son needs. As for us, we'll add bell pepper, onion, zucchini and maybe even chicken if we have some left over. Pair it with a salad and you have a fab lunch or dinner.
The benefit of making pizza at home is twofold. Threefold actually. It's fun to make, with or without the kids and yes, it takes more time but it's time well spent. It's done in just about the same amount of time it takes to preheat your oven. Next, is cost. The amount of money you give the pizza guy is likely double the cost of making it yourself. In our case, it's more than double. It is comparable to what a frozen pizza costs, sure but that leads me to the third benefit - knowing what the ingredients are and where they came from!
So before opening up the freezer door at the grocery store to fetch a pizza, consider grabbing the ingredients individually and making your own creation. I'm positive it will be affordable, fun, taste better and have a significantly higher nutritional impact than the frozen stuff.