You have to lock the bone before the transform is added, unlocking the bone will also force the avatar into the original position/size.
headbone = male.getBone("Bip01 Head")
headbone.lock()
trans = vizmat.Transform()
trans.setScale(0, 0, 0)
headbone.setMatrix(trans)
will probably do what you want, you do lose all animations on the headbone.
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