Sounds possible, though barely. A quick search hasn't found any sources for that, and I don't feel like wading through the millions of research papers about clean water, so I'm going to have to assume that this is untrue unless you can find sources. Good sources, because it goes in the face of all of the knowledge about the horrible things that unclean water cause [you're making the claim that there are "many cases" where people become sicker over the course of decades (or at least several years, due to the mechanism you point to) when they have clean drinking water. I think that I'm allowed to be skeptical].

EDIT: This sound similar to the "autoimmune diseases and allergies are due to a lack of parasites and other bacteria" theory (or is it still a hypothesis?).