Cut onion in half, then into thirds lengthwise before thinly slicing. Melt 2 tablespoons butter in sauté pan over medium low heat, then add onion and pinch of salt. Cook, stirring infrequently, until onions are golden brown, about 20-25 minutes.
While the onions are cooking, prepare macaroni, cooking 1 minute less than package instructs (generally 6 minutes). Drain and set aside.
Lightly butter 13×9-inch baking dish. Preheat oven to 350°F.
Melt remaining 2 tablespoons butter in large saucepan over medium low heat. Whisk in flour and cook, whisking occasionally, until mixture is smooth and bubbly, about 2 minutes. Add mustard, thyme, salt and pepper and cook 1 minute. Slowly whisk in milk, increase heat to medium, and cook, stirring frequently, until it begins to boil. Boil, stirring constantly, for 1 minute. Remove from heat and stir in Fontiago and pumpkin puree until sauce is smooth. Add caramelized onions and cooked macaroni and stir until pasta are evenly coated with cheese sauce.
Pour macaroni into prepared baking dish.