Toast quinoa in a dry, heavy skillet over medium heat until fragrant.
In a large saucepan or stockpot, melt 2 tablespoons butter over medium-high heat. Stir in onions, and cook until caramelized, about 6 to 8 minutes. Stir in quinoa, mushrooms, and molasses; cook until mushrooms release their liquid, adding a little chicken stock if necessary to facilitate cooking. Add remaining chicken stock, and bring to a boil; reduce heat to low, and let simmer for 18 to 20 minutes, or until quinoa is cooked.
Meanwhile, melt 1 tablespoon butter in a skillet over medium heat. Cook shiitake mushrooms in butter until softened; set aside.
Puree soup in a food processor or blender, and return to saucepan. Stir in cream, and heat (DO NOT BOIL). Season with salt and pepper to taste. Garnish with creme fraiche, shiitake mushrooms, and chives.