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.