We're not talking about finding the gene that causes brown hair, here, but a fundamental foundation shift (fundamental assumptions) on the order of discovering two plus two actually equaled 4.5 (just an example of the magnitude, not an assertion on my part).
Just as discovering a fundamental force which enabled FTL with little energy investment would overturn Relativity, there were fistfights in the aisles over Plate Tectonics vs Geosynclinal Theory. Fundamental change is met with strong resistance by those who have been taught the teachings of the status quo are gospel.
Minor advancements and refinements which are compatible with current fundamental theory are greeted (after peer review) as advancements.
Changes in the fundamental axiomatic structure of a field are resisted strenuously by those who have invested their lives in learning, researching, publishing, and teaching within the old set of axioms.
I can't remember when I heard or read that but someone was saying that the sun's effect on our gravity (or more probably, making a blip in our trip around the sun). That it appeared that the effects of the sun's gravity affecting Earth were quicker than it took light to make the same trip.
I wish I could remember where I read that.
I was lucky enough to have worked with one Nobel Laureate on a short project in grad school, and what impressed me the most was that he was ALWAYS questioning assumptions....his own, and others. And this was will into the twilight years of his career...he died a couple of years later.
I just wonder what Richard Feynman would have done if he had lived to see CF. Certainly his contemporary Julian Schwinger thought LENR was very real, and I think he was a bit shocked that he was actively prevented from publishing theoretical studies on the subject, despite his standing and credentials.
Here is an interesting discussion of points similar to those you make:
http://amasci.com/supress1.html