What is better: traditional medicine or pharmaceuticals?

Antibiotics also kill beneficial bacteria. My dad spent six months restoring his stomach flora after being treated for some illness with antibiotics.

Of course, they do. That's why a competent doctor
a) will never prescribe antibiotics without necessity;
b) will prescribe a drug to restore the flora of the stomach and intestines in conjunction with antibiotics.
Instead of antibiotics, antimicrobial drugs can be prescribed, but many doctors follow this path: let's use "heavy artillery," and then let the patient deal with the problems... But this is not a problem of medicines and chemistry, but of our poorly paid doctors, who don't care.
You can dislike medicines, but you can't ignore the facts: modern medicine has found ways to cure many diseases that were considered fatal in the last century. For example, most of them are saved by the much-disliked vaccinations. And no matter how you look at it, you can't make a measles or flu vaccine with folk remedies.