In a 2 quart sauce pan, combine quinoa and broth and bring to a boil. Reduce the heat to a simmer, cover, and let cook until all the liquid is absorbed, about 15 minutes. Remove from the heat and let rest 5-10 minutes.
Preheat the oven to 350ºF. Fluff the quinoa with a fork and transfer it to a large mixing bowl. Add the beans, broccoli, pesto, and 1 cup mozzarella cheese. Season to taste with salt and pepper. Stir to combine.
Spray a 9x13 inch baking dish with cooking spray and spread the quinoa mixture evenly in the dish. Top with the remaining cheeses. Bake 25 minutes or until the cheese is melted and beginning to brown. Serve garnished with halved cherry tomatoes, crushed red pepper flakes, and fresh basil if desired.