Actually the canard should not stall either---it is just getting on the other side of the peak (reduced lift----pitch bob) and gaining speed before a stall.
The vgs I used were installed aft of the 50% chord line----which if I understand correctly, won't screw with when it peaks but does keep the flow attached with moisture/dirt/bug contamination. Also, if I understand right, going forward of the 50% chord puts you in danger of doing what you said----upsetting the balance between the canard and main wing.
For what it is worth, the VGs completely tamed my GU canard----and "stall" testing went perfectly---nice pitch bobbing.