In medicine, John Ioannidis has basically built his career around exposing unpleasant truths that the perverse incentives have led the field away from. He has gotten several of his papers to various top journals, is currently a Professor of Medicine at Stanford, and been cited over 30,000 times. Isn't that evidence that you can make fundamental criticisms of the state of the field without sacrificing your career?
My intuition suggests that both in the case of Ioannidis and other somewhat similar cases - such as the WEIRD paper, which seriously questioned the generalizability of pretty much all existing psychological research, and which has been cited almost 300 times since its publication in 2010 - is that when a field is drifting away from reality, most of the people working within the field are quite aware of the fact. When somebody finally makes a clear and persuasive argument about this being the case, everyone will start citing that argument.
I certainly don't deny that the self-correcting mechanism you describe has worked to some extent in some fields in recent past. However, it also seems evident that in certain other fields nothing like that is happening, even though their mainstream has long been drifting far from reality, and the only people making cogent fundamental criticism are outsiders completely out of grace with the establishment. I don't have anything like a complete theory that would explain when correct fundamental criticism will be acclaimed as an important contribution, and whe...
Theism is often a default test of irrationality on Less Wrong, but I propose that global warming denial would make a much better candidate.
Theism is a symptom of excess compartmentalisation, of not realising that absence of evidence is evidence of absence, of belief in belief, of privileging the hypothesis, and similar failings. But these are not intrinsically huge problems. Indeed, someone with a mild case of theism can have the same anticipations as someone without, and update their evidence in the same way. If they have moved their belief beyond refutation, in theory it thus fails to constrain their anticipations at all; and often this is the case in practice.
Contrast that with someone who denies the existence of anthropogenic global warming (AGW). This has all the signs of hypothesis privileging, but also reeks of fake justification, motivated skepticism, massive overconfidence (if they are truly ignorant of the facts of the debate), and simply the raising of politics above rationality. If I knew someone was a global warming skeptic, then I would expect them to be wrong in their beliefs and their anticipations, and to refuse to update when evidence worked against them. I would expect their judgement to be much more impaired than a theist's.
Of course, reverse stupidity isn't intelligence: simply because one accepts AGW, doesn't make one more rational. I work in England, in a university environment, so my acceptance of AGW is the default position and not a sign of rationality. But if someone is in a milieu that discouraged belief in AGW (one stereotype being heavily Republican areas of the US) and has risen above this, then kudos to them: their acceptance of AGW is indeed a sign of rationality.