Well, while I can agree that the pharmaceutical industry has been permitted to influence drug use beyond what is appropriate, most of the reasons are political and legal, not medical. Direct to consumer advertising, paying for and occasionally suppressing clinical data, to name a few, are not in the public interest. But such activities were not promulgated by the NIH, FDA, or "organized medicine" (whatever that is). Dr. Angel, former editor of the New England Journal has recently published a book highly critical of the drug companies. I recommend it.
I do not agree that we are in a "dark age" where medicine is not open-minded. Many more new theories and findings are accepted today than ever before. Pasteur, Lister, Semmelweiss, et al. are not "outcasts", nor are the folks today who found that H. pylori was the cause of most ulcer disease - a very controversial but accurate view.
Our infant mortality rate is not rising, it is falling - down to 6.8 per 1,000 live births in most recent national data. And infant mortality is not an index of general population health, but of social and behavioral public health problems. Major risk factors for infant death are: no prenatal care; adolescent pregnancies; unmarried status; smoking. These are social, not medical issues.
I'm not sure what you mean by "everybody knows the cause of cancer..." Heredity, radiation and UV exposure, smoking, papilloma virus infection, benzene exposure, maybe Agent Orange are documented causes. Others are not yet proven. What is very clear is that aging is a major contributing factor. Anybody that can prove one cause will get the Nobel prize.
The FDA does not suppress homeopathy. In fact, FDA is prohibited by law from evaluating any homeopathic products for safety and effectiveness. Likewise, under the Hatch Act, manufacturers of dietary supplements do not have to show their products are safe, or effective. The FDA can remove them from the market only if FDA can prove they are unsafe.
It's not entirely true that "natural" products cannot be patented and manufactured as drugs. Many pharmaceuticals are derived from botanicals - e.g., vincristine (periwinkle), digitalis (foxglove), taxol (Yew tree bark), quinine, etc. I don't see it as inimical to the public that these products are produced in inspected facilities, with scientifically demonstrated effectiveness, and in known and predictable dosages. I'd rather have that than to go out in the backyard to pick foxglove for grandpa's heart failure.
If promoters of any alternative care can produce credible and scientifically defensible evidence of effectiveness, I will accept that. My concern is that for the most part they pitch unverified and usually unverifiable anecdotal or apocryphal allegations. Having said that, if someone gets leukemia or Hodgkins disease and wants to use homeopathic or naturalist products instead of chemotherapy, that's their decision and I won't arm wrestle them over it. Just don't ask me to pay for it.