To address what seems to be the misconception underlying your question:
Killing pathogenic bacteria is not what is difficult; killing them without harming their (usually human) host is.
This is why antibiotics are so precious:
They are drugs that affect only bacteria¹ – by exploiting properties that are unique to them.
It is usually resistance to ...
On a more budget-restricted level, when I worked in a high school, the science lab tech would take all the old Petri dishes out of a dedicated disposals freezer, and take them to the campus coal fired boiler.
Since the boiler only ran in Winter, there was a lot of stuff to dispose in the first few cold days in Autumn. As such, the science department ...
Autoclave at 120 degrees Celsius for 30 minutes. [ref]
Don't ever flush biological material, living animals, or anything other than sanitary-code approved waste down the toilet.
The proper way to dispose of used culture material is to sterelize it first, then dispose in sealed bags.
After counting, petri dishes should be secured in a plastic autoclave
Resistant to WHAT?
Scientists generally deal with bacteria resistant to some concentration of some particular substance (or combination thereof).
Those strains are still pretty much sensitive to great deal of other substances (e.g. etanol 70%), high temperature (boiling water at normal pressure or higher), etc generic ways to kill bacteria.
While people generally don't talk about bacteria losing antibiotic resistance, it does happen, and for a pretty obvious reason: the biochemical tools which confer resistance come at a metabolic/reliability/efficiency cost, or the bacteria would have had the resistance to begin with. In general, we can assume that bacteria are ...
You are absolutely right, flushing down the toilet (or the sink) or simply throwing them into the normal waste doesn't work for biosafety reasons. And it is also not allowed, depending on the country you would do this in, this can lead to hefty fines.
Biologically contaminated lab waste can be inactivated (=all potential dangerous organisms are destroyed) ...