Preheat oven to 350 degrees. Lightly spray a 3-quart casserole dish with cooking spray.
Heat the oil in a skillet over medium heat until fragrant. Cook the garlic for about one minute.
Add the onion, zucchini, and yellow squash, and season with garlic salt and thyme. Cook, stirring occasionally, for about 5 minutes.
Combine mixture in a large bowl with tomato, basil, prepared rice, and 1 cup of Gruyère cheese. Spread evenly into casserole dish and top with remaining cheese.
Bake uncovered for 20 minutes.
Enjoy!