Heat oven to 350°. Coat a 13 x 9 x 2-inch broiler-safe baking dish with nonstick cooking spray. Bring a large pot of lightly salted water to boiling. Add rigatoni and cook for 13 minutes, or as per package directions. Drain and return to pot.
Coat a large nonstick skillet with nonstick cooking spray and place over medium-high heat. Add sausage and cook 4 minutes, stirring until browned. Remove to a plate with a slotted spoon and keep warm.
Stir 1 tablespoon of the butter into same skillet. Add apples and onion and cook 5 minutes over medium heat. Remove from heat and stir in sausage, salt and pepper. Add to pasta in pot.
Meanwhile, melt remaining 2 tablespoons butter over medium heat in a medium saucepan. Whisk in flour and cook 1 minute. Pour in milk and mustard and bring to a simmer. Cook 3 minutes, whisking occasionally. Remove from heat and whisk in cheese. Stir into pasta mixture in pot.
Pour pasta mixture into prepared dish. Top with panko. Bake at 350° for 25 minutes. Increase oven temperature to broil and broil dish for 3 minutes until lightly browned.