Cook the quinoa in salted water according to the package directions.
Preheat the oven to 350 degrees. Spray a 9 by 12 inch baking dish with cooking spray.
Heat the oil in a large skillet over medium-high heat. Add the onions and cook until softened, about 5 minutes. Then add the garlic and cook another 30 seconds, stirring. Add the tomato paste and stir it into the vegetables; cook for 2 minutes, stirring. Add the canned tomatoes along with their juices, the Italian seasoning, 1 teaspoon salt, the pepper, and red pepper flakes. Cook for about 10 minutes, stirring occasionally. Add the heavy cream and 1/3 cup Parmesan cheese and cook, stirring just until heated through. Take off the heat and stir in the cooked quinoa, half the tomatoes, and half the basil. Pour into the prepared baking dish and top with the sliced mozzarella and the rest of the tomatoes.
Combine the remaining 1/3 cup Parmesan with the panko breadcrumbs. Sprinkle over the top of the casserole, spray with more cooking spray, and bake for 15 minutes or until the cheese is melted and the top is golden brown. Sprinkle with the rest of the basil and serve.