In a dutch oven or large heavy saucepan, melt butter over medium heat. Add onions, thyme and pepper; cook, stirring often, for 15 minutes or until onions are tender and a rich golden color. Blend in flour; stir in stock Bring to a boil, stirring until thickened. Reduce heat to medium-low, cover and simmer for 15 minutes.
Meanwhile, position oven rack 6 inches from broiler; preheat broiler. In a small bowl, combine olive oil and garlic; lightly brush oil mixture over both sides of bread. Arrange on baking sheet; place under broiler and toast on both sides.
Place toasts in deep ovenproof soup bowls; sprinkle with half the cheese. Arrange bowls in large shallow baking pan. Ladle hot soup in bowls. Sprinkle with remaining cheese. Place under broiler for 3 minutes or until cheese melts and is lightly browned. Serve immediately.