imagine the trauma a fish would go through to be removed from its tank water, put into a water system filled with chlorine/chloramine (if you're in a city, even if not theres at least amounts of toilet bowl cleaner). If that wasn't even to burn their gills (stick ur head in a bucket of powdered chlorine, like at a pool, it sucks let me tell you) and cause death, then then go down a crazy series of tubes to be eventually dumped into a massive sewer treatment. I doubt the water can be considered "clean" to something which is breathing it. Even if it is considered clean by human standards, that means it is being filled with chemicals which are meant to kill off any harmful bacteria, chemicals which seriously mess fish up. It is a horribly cruel way to end a fish's life, and you can only pray that the amounts of cleaner in the bowl or the shock of going down a whirlpool kill the fish before anything else does.
if you're merely talking about flushing a dead fish...no worries, although if the fish had tb i wonder what damage that could do...