Preheat oven to 400°F. Spray 13x9-inch or shallow 3-quart baking dish with cooking spray. Stir together drained tomatoes and pesto in small bowl; set aside. Combine uncooked macaroni, fontina cheese and 1 cup mozzarella cheese in large bowl. Place in dish in an even layer.
Microwave 4 tablespoons butter in large microwave-safe bowl on HIGH 30 seconds or until melted. Whisk in milk, flour, salt and pepper until blended. Pour over macaroni mixture. Spoon tomato mixture evenly over macaroni. Cover dish with aluminum foil; bake 40 minutes.
Meanwhile, microwave remaining 2 tablespoons butter in small microwave-safe bowl on HIGH 20 seconds or until melted. Stir in bread crumbs. Top macaroni with remaining 1 cup mozzarella cheese and bread crumb mixture. Bake uncovered 10 to 15 minutes more or until golden brown on top. Let stand 5 minutes before serving.