Please don't drive yourself crazy over this ... try not to take meds right with your Miracle-Mineral-Supplement . But, the only thing that will counteract it is a strong antioxidant. If you take meds almost concurrently with Miracle-Mineral-Supplement , you may find that your stomach becomes upset, as you described.
But, if you separate them by just a little while, I dont think you will notice anything at all negative.