I agree that the net benefit of medicine is not nearly as high as many assume. I wrote a lengthy article on the meta research that describes the problem.
That said, it seems over-reaching to suggest that EBM doesn’t ask the ethical questions of net benefits, inclusive of negative impacts. The calculus is made explicit, albeit imperfectly, in aspects such as number needed to treat, likelihood ratios, etc., is it not? These methods have been criticized as being insufficient, particularly in light of the overwhelming attention placed on confirmatory evidence. Are you saying that these matters are not incorporated in the EBM framework?
I agree that EBM lacks the tools to handle the problem. But the question I ask is, Why are so many interventions found to be harmful only after they’ve moved into mainstream use? Why are clinicians armed with such a mixed bag of remedies in the first place? The primary ethical assault is in the production of bad biomedical research and the flawed products derived from same.