In a nonstick saucepan, heat 1 tablespoon butter over medium heat. Add onion, and cook until softened, about 8 minutes. Place milk and flour in a jar with a tight-fitting lid. Shake vigorously to combine; pour into saucepan, and cook over medium-high heat, stirring constantly, until mixture thickens and bubbles, about 7 minutes. Stir in pizza sauce, and remove from heat.
Place tomatoes and remaining 1 teaspoon butter in a microwave-safe bowl, and microwave for 1 minute. Stir; microwave 1 minute more.
Place pepperoni and cooked pasta in a large serving bowl; toss with sauce and tomatoes.