This is maybe eventually going to be an essay about how to deal with those cases where there is a significant opinion expressed by a minority community about possible bias or misstatement of fact by a more dominant expert opinion in the same field, possibly related to some sort of financial, academic, or philosophical/religious biases on one part or the other. Anyone who wants to add anything at the early stages here is free to do so, either by drafting here or commenting on what might be included on the talk page.
Have at it, y'all.
Best sources
In many cases involving scientific or academic controversies, there will be multiple well-regarded academic reference sources discussing the topic. In general, although there will always be exceptions, it is not unreasonable to assume that most of the major viewpoints will be discussed in at least one of them. That being the case, it might well be best, under the circumstances, to seek, through WP:RX and other means, as many such sources, perhaps particularly of an encyclopedic or dictionary nature, and find what material they include in the directly relevant articles. Particularly for those encyclopedic sources covering a wide subject, such as for instance philosophy, religion, or science, it is not unreasonable to expect that at the very least the divergent material in such broad-based reference works be included to a reasonable degree in the main article.
And, particularly for areas of contention where there are questions as to whether the "best practices" of a given discipline may not be being followed by those advocating the mainstream or majority academic opinion, and there is some reasonable support for that position in academic sources independent of the advocates of that minority view, material as to why on what basis the existing dominant viewpoint is challenged might reasonably be considered.
In those rarer cases where there the minority opinion is challenging the dominant opinion on matters which may not yet have had sufficient time for alternative views to be supported, such as questions about long-term medical effects in topics where no long-term results are specifically available yet, where there is substantive discussion of that lack of evidence in the sources that material should be presented at sufficient weight in the main article to make it possible for the average reader to understand the point of disagreement and how on that basis no clear refutation is necessarily possible yet.