I don't know much about the technical end of running a spa. Our pool maintenance man does what it takes to keep things stable, as well as satisfying the health department. The water quality in our county is just plain nasty (salt/calcium/and who knows what) compared to what we're used to up north, and heavy on the chlorine is standard procedure in the desert. You can smell it just standing at the toilet. We wouldn't even consider drinking it, but at least I feel real sanitary when I get out of the hot tub.
There's no getting around the chlorine and chemical factor - just working around it is the vest we can do.