Avorn (2004) reports:
In a former British colony, most healers believed the conventional wisdom that a distillation of fluids extracted from the urine of horses, if dried to a powder and fed to aging women, could act as a general tonic, preserve youth, and ward of a variety of diseases. The preparation became enormously popular throughout the culture, and was widely used by older women in all strata of society. Many years later modern scientific studies revealed that long-term ingestion of the horse-urine extract was useless for most of its intended purposes, and that it causes tumors, blood clots, heart disease, and perhaps brain damage.
The former colony is the United States; the time is now; the drug is the family of hormone replacement products that include Prempro and Premarin (manufactured from pregnant mares' urine, hence its name). For decades, estrogen replacement in postmenopausal women was widely believed to have "cardio-protective" properties; other papers in respected medical journals reported that the drugs could treat depression and incontinence, as well as prevent Alzheimer's disease. The first large, well-conducted, controlled clinical trial of this treatment in women was not published until 1998: it found that estrogen replacement actually increased the rate of heart attacks in the patients studied. Another clinical trial published in 2002 presented further evidence that these products increased the risk of heart disease, stroke, and cancer. Further reports a year later found that rather than preventing Alzheimer's disease, the drugs appeared to double the risk of becoming senile.
Armstrong (2006) adds:
The treatment seemed to work because those who used the drug tended to be healthier than those who did not. This was because it was used by people who were more interested in taking care of their health.
Though keep in mind that it's much more complicated than "Haha, some idiots were drinking chemicals from horse urine but now we know better."
HRT is "undoubtedly" effective for hot flashes, osteoporosis, and atrophic vaginitis. It's probably effective against some cancers. It may be effective against heart disease and dementia when taken in the first decade after menopause, but not after (the women in the study you mention were mostly in their 60s). However, all of the risks mentioned here are very real and so HRT is not indicated except when people have premature menopause or unusually severe menopausal symptoms (these people should talk to their doctors about it)
Also, why title this "Why We Need Better Science"? Sounds to me like we have great science, we just need people to hold their horses (pun not intended) until the results come in instead of chasing after every therapeutic fad.