Score bottom of each tomato with an "X." Bring 2 quarts water to a boil in a Dutch oven. Add tomatoes; cook 30 seconds. Remove tomatoes with a slotted spoon; plunge tomatoes into ice water. Drain and peel. Cut each tomato in half crosswise. Push seeds out of tomato halves using the tip of a knife; discard seeds. Chop tomatoes.
Cook pasta according to package directions, omitting salt and fat; drain. Toss pasta with 1 teaspoon oil. Cool completely.
Heat 1 tablespoon oil in Dutch oven over medium-low heat. Add onion; cook 7 minutes, stirring occasionally. Add garlic; cook 3 minutes or until onion is tender, stirring frequently. Stir in tomatoes, 1 cup water, parsley, chives, oregano, thyme, and broth; bring to a boil. Reduce heat, and simmer 20 minutes, stirring occasionally. Add pasta, vinegar, and pepper; cook 1 minute or until thoroughly heated.
Place bread slices on a baking sheet, and top each slice with 1 tablespoon cheese. Broil 1 1/2 minutes or until lightly browned. Serve with soup. Garnish with thyme sprigs, if desired.