Preheat oven to 350 degrees F. Coat a 2-quart baking dish or casserole with nonstick cooking spray; set aside.
Cook pasta according to package directions in a large saucepan. Drain and return to saucepan; set aside.
Meanwhile, in a medium saucepan whisk together milk and flour. Cook and stir over medium heat until thickened and bubbly. Cook and stir 1 minute more. Remove from heat. Stir 1/2 cup of cheese, salt and hot pepper sauce into the milk mixture until smooth.
In the large saucepan toss together the cooked pasta, apples, kielbasa and cheese sauce. Transfer to prepared baking dish; cover with foil.
Bake in preheated oven for 20 minutes. Uncover and carefully stir pasta mixture. Sprinkle with remaining 1/2 cup cheese and the green onion. Bake 10-15 minuted more or until cheese is melted and sauce is bubbly. Remove from oven and let stand for 10 minutes before serving.