Cerebus Pu hit it on the head.
Botulism by definition is being exposed to the neuro toxin produced by the bacteria, not the bacteria itself which is easily neutralized by an acidic environment, and since Chlorine is an acid, treating the water supply with CH3 (I think thats the abreviation) would do away with the bacteria itself.
The real threat is "botulinum toxin"
"Botulinum toxin attacks nerve endings, permanently damaging them. It can't cross the barrier that protects the brain. The heart has its own wiring system and also isn't affected. However, botulin can affect all the other nerves of the body, including the nerves of the muscles that operate the lungs. Botulin toxin kills by shutting down breathing. "
"Unfortunately, these bacteria secrete a neurotoxin (nerve poison) so deadly that a few billionths of a gram could kill you. This is botulin toxin, one of the most dangerous substances known. Botulism is the condition of having been poisoned with botulin toxin."
Heres an interesting read on how difficult it would be to use Botulism as a Bio Warfare Agent
Yes and even more difficult in a municipal water supply.