Coat a Dutch oven with cooking spray; add margarine. Place over medium heat until margarine melts. Add onion and garlic; saute 5 minutes or until tender. Add flour, stirring until smooth. Stir in chicken broth and next 4 ingredients; bring to a boil. Cover, reduce heat, and simmer 45 minutes or until squash is tender. Let cool.
Position knife blade in food processor bowl; add squash mixture. Process 1 minute or until smooth, scraping sides of processor bowl once.
Return mixture to pan; add milk. Cook over medium heat until thoroughly heated, stirring occasionally. Ladle soup into individual bowls. If desired, garnish with squash seeds, thyme sprigs, and sour cream.