Preheat oven to 350 degrees F (175 degrees C). Lightly grease a large casserole dish.
Bring a large pot of water to a boil. Place the macaroni in the pot, cook 9 to 11 minutes, until al dente, and drain. Transfer to the prepared casserole dish.
In a skillet over medium heat, cook and stir the ground beef and onion until beef is evenly brown and onion is tender. Stir in the wine, and continue cooking 1 minute. Mix in the milk, mustard, and Worcestershire sauce. Season with salt, pepper, and cayenne pepper. Continue to cook and stir until heated through. Whisk the flour into the skillet, and gradually stir in 2 cups cheese until melted. Mix in the thyme and cherry tomatoes.
Stir the skillet mixture into the casserole dish with the macaroni. Top with remaining cheese.
Cook uncovered 30 minutes in the preheated oven, until bubbly and lightly brown.