If the disinfectant in your water supply was strong enough to kill off your nitrifying bacteria you wouldn't be able to drink it, but it would probably make a great oven cleaner! Plenty of folks do a 25% water change with municipally supplied water without any problem. One issue municipal water suppliers are up against are bacteria in the system that are more resistant to chlorine/chloramine, and split the ammonia from chloramine using it as a food source. It's easy to get these bacteria to grow in your filtration system, as they come in with your water supply.
With this issue, if suppliers increase the chloramine, they increase the food source, thus increasing the bacteria. What they do, and what has been working somewhat is breakpoint chlorination. They'll give the whole system one massive dose of disinfectant, in the hopes of knocking it back. They give a heads up to folks on the system, not just because of fish, but the water is like drinking from a heavily chlorinated swimming pool.
