Preheat oven to 375 degrees F. Heat a large nonstick skillet over medium heat. Add 4 teaspoons oil; swirl to coat. Add onion and cook 3 minutes. Add bell pepper; cook 2 minutes. Add squash and garlic; cook 4 minutes. Place vegetable mixture in a large bowl. Stir in cooked quinoa, 1/4 cup basil, thyme, 1/2 teaspoons salt and black pepper.
Combine remaining 1/4 teaspoons salt, milk, cheese and eggs in a medium bowl, stirring with a whisk. Add milk mixture to vegetable mixture, stirring until just combined. Spoon mixture into an 11 x 7 inch glass or ceramic baking dish coated with cooking spray.
Place bread in a food processor; pulse until coarse crumbs form. Return skillet to medium-high heat. Add remaining 1 teaspoons oil to pan; swirl to coat. Add bread crumbs; cook 3 minutes or until toasted. Arrange tomatoes evenly over vegetable mixture . Top evenly with bread crumbs. Bake at 375 degrees for 40 minutes or until topping is browned. Sprinkle with remaining 1/4 cup basil.