Cody - waste water facilities are designed to deal with all manner of things that go down the drain. I'd say a dead fish is a hell of a lot cleaner and better than the other stuff we normally flush down the toilet. You don't throw your poo in the trash do you? A water plant deals with both in the same manner, there are grinders, skimmers, digesters and settling tanks for a reason. The bacteria that are cultured in the tanks of a waste water plant eat all forms of dissolved solids, poo or dead fish makes no difference to them. If anything the fish is probably easier for these bacteria to break down than some of the stuff you'll find nowadays in human fecal matter.
I'd be far more worried about the amount of drugs, prescription and illegal, that you will find in effluent than I would some dead fish. The fish aren't a problem to deal with, we already know how to do that. The easily measurable amounts of heroine, cocaine, meth and viagra should be far more concerning to you. The bacteria don't break those down, and they are often extremely difficult to filter back out of the water. It's not the dead fish that went down the toilet that are causing the frogs in your local waterways to grow extra legs, it's the meds that humans consume, and then pass back out of their system through urine and fecal matter.