Preheat oven to 375˚F. Lightly grease a 9x13 baking dish with cooking spray and set aside.
Cook the orzo according to the directions on the package. Meanwhile, heat 1 tablespoon olive oil in a large skillet set over medium heat.
Add the zucchini to the heated oil and season with Italian seasoning, ¼ teaspoon salt, and pepper. Cook for 5 minutes, or until zucchini is crisp-tender.
Remove zucchini from the pan and transfer to a large mixing bowl. To the same bowl, add the drained cooked orzo; stir and set aside.
Return skillet to the burner and heat remaining olive oil over medium-high heat. Add in the onions and cook for 1 minute. Stir in the garlic and cook for 20 seconds.
Stir in the ground beef, breaking it up with a wooden spoon. Season with remaining salt and cook for about 6 to 7 minutes, or until the ground beef is completely browned and cooked through.
Drain fat, if any, then add the beef to the large bowl with the orzo and zucchini.
Stir in the crushed tomatoes, ½-cup mozzarella cheese, ricotta cheese, parmesan cheese, basil, and thyme. Stir until everything is well combined and cheeses are melted.
Transfer the mixture to previously prepared baking dish and top with remaining mozzarella cheese.
Bake for 20 to 25 minutes, or until casserole is bubbly and cheese is melted.
Remove from oven and let stand 10 to 15 minutes.
Garnish with basil and serve.