It's not so much about going blind, Izanagi effectively closes the eye forever, EMS or no EMS; the price for using that technique is handing over an eye, not so much "going blind".
If EMS countered this, there would be absolutely no point in even trying to fight someone with EMS/Izanagi; the madara/5kage fight would be incredibly pointless cause madara could just stand around while constantly just tanking their attacks, effectively making them wear themselves out and then just walk in and decapitate them 1 by 1.

Izanagi makes you untouchable, but only for as how many eyes you have. EMS countering that aspect would effectively be turning on "god mode".