The dilemma really seems to be related to the increasing commercial entanglement of medicine as you said. It is a trade-off between speed of research in discovering ever so more complex, specialized and effective treatments (which is highly desirable) and scientific integrity. One saving grace though is the ability to aggregate several studies on the same topic into a meta-study which may assess and improve the significance of results. In important trials this is done very frequently.
Judging from other fields of science I would also not be surprised if some journals did not uphold their standards of due diligence as much as one might expect. There is a lot of money and influence involved in scientific publication and one might accuse some publishing companies to prioritize commercial interest over scientific.