I have never made meds. But it seems to me there has to be a way to make them without deleterious side effects. Right?

Those meds without side effects are found in nature.  To get a patent and make billions,  the natural form must be altered into a unique substance to be patentable.  These unnatural substances might even seem to work better than nature, but the side effects are the cost...  That and the extra we pay at the pharmacy for something like a prescription antibiotic versus lomatium dissectum.