For the compote: In a small saucepan on medium-high heat, add the cherries, wine, salt, pepper and thyme and stir. Bring to a boil, then reduce the heat slightly to medium. Continue to cook at a rapid simmer until the liquid is reduced by half, 25 to 30 minutes. Turn off the heat and let cool, then remove the thyme sprigs.
For the baguette: Preheat the oven to 400 degrees F.
Using a paring knife, cut a deep "v" on the top of the baguette. Pull out some of the soft bread to create a deep crevice. Place the Brie slices into the crevice, overlapping each slice. Transfer to a baking sheet.
Bake until the cheese is melted and the bread is slightly toasted, 5 to 7 minutes. Transfer to a cutting board. Spoon the cherry compote over the melted Brie. Slice into thick slices, garnish with the remaining thyme sprig and serve.