Simply put, armor was created to counter mass CC being op. So the obvious solution is to make armors do that and only that. Make knockdown and stun effects do a small amount of secondary phys or magic stun damage to the armors until they break. After the stun is over, the bar that broke refills. If you wanted to encourage mixed magic/phys play, just make the phys or magic armors bars get larger with every recovered stun in a battle. Knockdown a guy a few times and doing it again will be much harder, but stunning him won't be.
This would also fix the players getting chain stunned because they got surprised in a bad position unavoidably. (happens alot).
