Preheat the oven to 400°F. Place the squash in a 9 x 13-inch baking dish, drizzle with 1 tablespoon of the oil, and season with the salt and pepper. Roast for 40 minutes, until fork tender.
Meanwhile, heat the remaining 1 tablespoon oil in a large saute pan and saute the onion with the thyme for 5 minutes. Remove from the heat and set aside; discard the thyme sprigs.
Remove the squash from the oven and carefully transfer to a blender or food processor. (If using a blender, remove the center of the lid to allow steam to escape and cover the hole with a towel to prevent splashing.) Blend the squash with the sauteed onion, vegetable broth, crème fraiche, and cinnamon until smooth. Pour the soup into the saute pan and heat through.
To serve, ladle a generous 1-cup portion of the soup into each of 6 bowls. Top each serving with a teaspoon of crème fraiche, if desired.