Back in the day when Herr Hahnemann was alive people also used amulets to protect themselves and they'd still occasionally brutalize old women for being "witches".
Homeopathy has lasted longer than amulets for the most part (though "good luck charms" are amulets as well, and some people still have those), but it's a child compared to the ancient, but useless, art of astrology. Despite astrology being bunk, it's lasted for many millennia because people delude themselves into thinking it works. Antiquity is no guarantee of authenticity, especially when dealing with science.
The truth is that homeopathy probably does work—but only in the way placebos work—people took the medicine that supposedly had the "essence" of certain healing substance in it, and because they expected to feel better afterwards, they did. (Often, the substance supposedly doing the work would so diluted that the actual physical presence of that substance was reduced to zero, but homeopathy is fine with that because the "essence" can be transfered to the medicine even if there are zero parts per million of the substance that's supposedly curative).
It is, in every conceivable way, no different than drinking "magic potions" and expecting those to work.
As for real medicines that have gone by the wayside, you overstate things tremendously. *Some* medicines have been pulled for being dangerous. Many more medicines that made it to the market in the past 80 years (and before then I agree that there were a lot of bunk medicines mostly because the sorts of doctors ho invented them were of a non-scientific, often homeopathic, mindset) were replaced because they had side-effects and better medicines, that treat the same condition with fewer or more manageable side effects were discovered. Other times alterative medicines were developed because certain people have severe negative reactions to a given drug, so alternatives were needed for those people.
I would not say that homeopathy and folk medicine had no good effects though. Some of the folk remedies they relied on turned out to have some merit and were incorporated into modern scientific medicine and were generally made more effective in the process. Aspirin itself may be a form of that, as some used to prepare willow bark in a way that supposedly treated headaches, and willow bark does contain some acetylsalicylic acid.
The stuff that had no value was by and larged looked at and discarded. "Allopathic" medicine is not per se *opposed* to homeopathy, so long as there is evidence that it works. That proof, shown in repeated trials of the treatment, is that mark of "science." If homeopathy showed incontrovertible success in such tests, then the effective treatments would drift over into modern, scientific medicine (which is what "allopathic medicine" really is).
I understand that you feel that homeopathy is better, but such a feeling is not a useful scientific criteria. I understand that you feel that because homeopathy uses natural substances that it must be "safer", but most poisons that are naturally occurring substances. Posons have also been around for many, many millennia, and artificial poisons only about 150 years. "Natural" does not mean "safe" and it certainly does not mean effective.
Again, though, to the extent you or anyone else feels that you have a natural and effective treatment for an ailment, you are fee to research it, test it, publish your findings, wait for others to test it in the same way as other science is tested. If you are right, "allopathy" will gladly embrace your findings. Scientists are generally cool like that.