Heat oil in a large saucepan over medium heat. Add onion and garlic, and sauté until lightly softened, about 3 minutes. Stir tomato paste and flour into onion for 1 minute. Slowly whisk in milk and broth to avoid lumps. Stir in tomatoes and season lightly with salt and pepper. Bring to a simmer and cook, stirring occasionally, for 10 minutes.
Using a hand blender, purée soup until smooth. Press through a fine mesh strainer to remove seeds. Return soup to pan and bring back to a simmer. Stir in Worcestershire sauce and 3/4 cup cheese until melted.
Ladle soup into bowls. Garnish each with remaining cheese and fresh thyme leaves.