That's unusual. Could you look again at the new growth. If it is definitely above the join it won't be the rootstock, but this sort of occurence is what happens when a graft fails, and the new growth emerges just below or on the join. If you are sure it is above the join then you could prune it back to the new growth and train one shoot to be a replacement main stem. But if it were me I wouldn't bother. For all the effort, and the risk that it will fail, or that it may turn out in years to come that it IS the rootstock.I'd try and get a replacement. Last weekend I saw them cheap in (or outside, rather) Poundland or Poundstretcher - can't remember which.