Bring a large pot of lightly salted water to a boil. Cook elbow macaroni in the boiling water, stirring occasionally, until cooked through but firm to the bite, 8 minutes; drain.
Melt butter in a separate pot over medium heat. Cook and stir sausage and onion in melted butter until the onion is translucent, 5 to 7 minutes.
Stir tomatoes, green bell pepper, yellow bell pepper, orange bell pepper, red bell pepper, basil, thyme, and oregano into the sausage mixture; continue to cook and stir until the peppers have softened, 5 to 7 minutes. Add drained macaroni; bring to a simmer and cook another 5 minutes. Pour the mixture into a 2-quart casserole dish and top with cheese cubes.
Bake in preheated oven until the cheese has melted, about 5 minutes. Stir melted cheese through the macaroni mixture, pat the mixture down into a flat layer, and continue baking until heated through, 10 to 15 minutes more.