I don't think that Chlorine Dioxide makes it into your tap water at home. It is used as a PRE-decontamination before they add regular Chlorine. Just dumping Chlorine into the water will result in it mixing with other contaminates and forming toxic substances. Chlorine Dioxide is a very energetic little molecule and will have burned itself up by the time the water gets to you, otherwise they would not need to add Chlorine.
As for Malaria, it is mostly a blood borne disease and I think Miracle-Mineral-Supplement is very quick to knock out diseases in the blood, it being the first thing it comes into contact with besides the stomach.