Combine first 11 ingredients in a large saucepan; bring to a boil. Cover, reduce heat, and simmer 30 minutes, stirring occasionally. Uncover and cook for 5 minutes or until slightly thick, stirring occasionally. Cool.
Preheat oven to 400°.
Divide Brie slices into 40 even pieces. Spread 1 1/2 tablespoons compote over each baguette slice; top each with 1 piece of cheese. Arrange the slices on a large baking sheet. Bake at 400° for 5 minutes or until cheese melts. Garnish with thyme sprigs, if desired.