Is non-evidenced based medical care any different from alternative modalities?

Dr. R. W. Donnell recently exposed the promotion of pseudoscience among medical students and, as was also written here, financial benefits can be powerful incentives for mainstream medical professionals to put out shingles selling diets, supplements and alternative modalities. He just posted a poignant rebuttal to assertions that alternative woo is no worse than non-evidence-based conventional medicine. There are very real differences, as he explains:

Why focus on woo?

...As I tried to explain in this post one important difference lies in the area of scientific plausibility: “Although some conventional methods fail to measure up to best evidence they are at least based on known anatomy and physiology. They have some plausibility in the observable biophysical model in contrast to the ‘vital forces’, nebulous ‘energy fields’ and ‘non-local powers of the mind’ which are characteristic of woo.” Viewed in that context they can hardly be construed as “competing mythologies.”

The commenter needs to understand that although I want doctors to practice evidence based medicine my focus is not on what individual doctors do. It’s the hypocrisy of mainstream medical institutions (journals, medical schools, hospitals) claiming to be all ethical and evidence based while promoting unscientific and even fraudulent claims that has my attention....