There is no good way to stop the queen from going into the higher supers,
buy once you have the bees working in them and a few combs drawn out, put
the excluder in, that will stop her.  The advice you got about not using a
queen exclduer with new undrawn comb is very accurate.  Evenif you get a
few larvae and eggs in the honey supers, they will filter out. Ug!  So does
everything else.