You've identified a situation that was/is all too common in the sciences. As theories have evolved and been subjected to systematic observation and testing feathers have been ruffled. A classic example of that is with the whole idea of "balance" in nature. Scientist Frederic Clements had a theory about "Climax communities," in which the plant and animals would evolve to a point at which it would sustain itself at that highest level. This was a popular theory for quite a while, but it was eventually set aside. Donald Worster in Nature's Economy: A History of Ecological Ideas states

Despite his more pragmatic admissions, Clements' doctrine of the climax as a natural ideal was by now firmly lodged in the national imagination. And Clements himself could not surrender his admiration for this long-enduring communal order, this complex super-organism nicely adjusted to the vagaries of climate. This feeling created a dliemma for both the man and the nation, not an easy one to resolve. (237)

As scientists came along and disproved his conclusions Clements didn't concede gracefully. I don't have time to reread that section of the book to spell out the events, but in the scientific world it wasn't a pretty thing to watch.

SRS