On a work surface, place the onion, orange, garlic, and rosemary in the duck cavity. Place it breast side up in a large skillet or Dutch oven. Brush with the honey and sprinkle with the thyme leaves. Season with salt and pepper. Cover with a sheet of aluminum foil and bake for about 30 minutes. Remove the foil and continue baking for about 2 hours and 45 minutes, basting frequently with the pan juices.