In a large pot, melt butter over medium-high heat, add onion, thyme, bay leaves. Cook covered for 15 minutes, stirring regularly to lightly caramelize. Add flour and cook 1 minute. Add milk and broth, season, cover and cook 15 minutes over medium-low heat.
Remove the thyme stems and bay leaves. Purée soup using blender until homogenous. Rub one side of toasted baguette rounds with garlic and sprinkle with cheese. Place under grill until golden. Serve the crostini with the soup.