a quick rinse under the tap shouldn't hurt the bacteria enough to cause all that.
chlorine takes a long time to work as a disinfectant.
unless you let your media soak for minutes and minutes, it won't hurt anything.
I think it was the hoses that did it.
I too rinse my filter under tap water, and have been doing so for years.
its only when I took courses in chlorine training (used to use it for wastewater treatment where I work) that I realized why it didn't hurt anything:
the contact time is not sufficient with a quick rinse under the tap.