I don't know of any natural sedatives, and I suspect if she is that upset you might need a prescription one anyway you get the effect you want.
Can you have someone else hold her for you? Gently, yet firmly, close her wings. Then keep your hand behind the joints that are kicking and she won't be able to move them. Also sometimes you can make the joint not move by making a fist enclosed over the joint. Other people have success by wrapping a towel around their ducks to keep their wings closed. Turn your duck into a burrito!