Combine carrots, broth, 1/2 teaspoon thyme, and garlic in a large saucepan over medium-high heat; bring to a boil. Reduce heat, cover, and simmer 10 minutes. Place carrot mixture in a blender; process until smooth.
Place flour in pan. Gradually add the milk, stirring with a whisk until blended. Add pureed carrots and ground nutmeg; stir to combine. Bring to a boil. Reduce heat; simmer 5 minutes, stirring constantly. Remove from heat, and stir in 1/4 teaspoon thyme, butter, salt, and lemon rind.