"It makes it seem as though there was just the Good side that had all the answers all along"

That, right there, is where so many people went wrong and what was blatantly exploited by grifters up and down the chain. The side of science didn't "have answers all along", but it was willing to learn and change.

And no, it wasn't "boo science". It was, to a large extent, political maneuvering using science as a convenient scape goat, because whenever science learned, it got turned into a "see, they don't know either". And, of course, with a large helping of grifters making money off the ensuing confusion.

In reality, it came down to seeing who was willing to change their mind in the face of new evidence, and it was a pretty clear signal. (It was not noise free, absolutely, but it was not extremely hard to read, either - if folks had a basic amount of scientific education. There's your solution, too)

There is no solution to this other than massive investment in education. And that isn't going to happen in our current world.