Preheat oven to 350ºF. Grease a large casserole.
Cook pasta al dente in boiling salted water.
In a deep skillet, melt butter over medium heat. Add onions and garlic and cook until soft, about 5 minutes. Add flour and stir to form a paste. Cook for 2 to 3 minutes. Slowly whisk in milk until smooth. Whisk in 1 cup of cheese. When cheese is melted, add pumpkin and sage. Season with salt and pepper.
Mix pumpkin mixture with pasta and spread in prepared dish. Mix together remaining cheese and bread crumbs and sprinkle on top.
Bake for 30 minutes, or until topping has browned.