10-20ml of CS rectally will not penetrate deep into your colon and affect your good bacteria. You have many yards of instestines so I doubt your good bacteria will be affected. You are not doing an enema, less than a tablespoon of CS.
The CS will get to your liver and kill off any nasty parasites, bacteria or viral nasties in your liver. Similar to the herbs recommended in liver flushes.
I would also look up coffee enemas
and if used that would dilate the ducts in your liver and gallbladder, and help your liver purge any dead nasties.
I also recommend using the CS about 4 times a day initially. You may have some herz effects (loose stools etc...) Continue CS use until everything is normal.
Supplementing with oral and sublingual use with also be beneficial and improve the hygiene of the throat and mouth.