I don't buy that explanation. Condensate in A/C are, as far as I know, pretty clean water when compared with sanitary water. In fact if you divert condensate into the sanitary water you have a dilution effect. As many polution level measures are in units/lt, in fact you should need less chemicals and treatment, as you are putting cleaner water in the line.
Why don't you inquiry the County directly? Eventually this is one of those regulations that is forgotten and nobody knows exactly the reason...