Yes the Clorox toilet bowl cleaner with bleach is safe to use in Septic Systems and breaks down mostly to water and salt pretty quickly.
So the Clorox toilet bowl cleaner with bleach will not mess with any good bacteria in your septic system as long as you do not use a lot of it at a time.
Just use enough of the Clorox toilet bowl cleaner with bleach to clean the toilet and your septic system should be just fine.
I used to have a septic system and used Clorox Bleach and other Clorox cleaning products in my sinks and toilets all the time and never had a problem with the septic system when doing so.