Melt butter in a 3-quart saucepan over medium heat; add onion, and cook 5 minutes, stirring constantly, until tender. Add cauliflower and next 4 ingredients. Bring to a boil; cover, reduce heat, and simmer 15 minutes or until cauliflower is very tender.
Combine half-and-half and flour, stirring with a whisk; add to cauliflower mixture. Bring to a boil; reduce heat, and simmer 2 minutes, stirring often. Remove and discard thyme. Cool 15 minutes.
Place half of cauliflower mixture in a food processor or blender; process until smooth. Pour pureed mixture into a large bowl; repeat procedure with remaining cauliflower mixture. Ladle into bowls; sprinkle each with cheese.