if you scaled the hierarchy under a group node, then I am afraid it is impossible to get this topNode lost. if you find a way don´t hesitate to tell me how you did it (not in case you just gave the rootbone the same scaling values then the groupNode has
you can move the bones around (using MMB) inside the group at any time. and if I am not wrong MotionBuilder doesn´t have a problem importing hierarchies with a null group on top of all.
everything starts and ends in the right place at the right time.