(Optional) Heat oven to 350 degrees F.
Bring a large pot of salted water to a boil. Cook macaroni as directed on package.
While macaroni is cooking, melt butter in a medium saucepan over low heat. Add flour and stir for 1 minute. Remove from heat and stir in milk.
Place back onto heat and bring to a simmer. Stir for 1 minute or until the mixture has thickened.
Stir in salt, pepper, nutmeg, mustard, and pumpkin puree. Add 2 cups of cheese, and stir until the cheese has melted.
Drain macaroni, and then add it into the cheese sauce. Stir until coated. You can serve the macaroni now or you can bake the pasta with the remaining cheese.
(Optional) To bake the pasta, pour it into a 3-quart casserole dish and then top it with the remaining 1/2 cup of shredded cheese. Bake uncovered for 20 to 25 minutes or until golden brown.