Combine onion, 1/2 cup wine, sugar, 1 teaspoon thyme, and 1/4 teaspoon black pepper in a large Dutch oven. Cover and cook over medium heat 20 minutes or until onion is soft, stirring occasionally. Add vinegar; cook, uncovered, 15 minutes or until liquid almost evaporates and onions are caramelized. Remove 3/4 cup onion mixture; set aside.
Sprinkle the veal with 1/4 teaspoon black pepper. Add 1 cup wine, 1 teaspoon thyme, veal, broth, red pepper, tomatoes, and garlic to pan; bring to a boil. Cover, reduce heat, and simmer 1 hour and 15 minutes, turning veal occasionally. Uncover and cook for 30 minutes. Stir in pasta and beans; simmer 15 minutes or until pasta is tender. Serve with the reserved onion mixture, basil, and lemon zest.