> what evidence do we have to believe that we haven't made some of the same mistakes in classifying pseudoscience in the present?

The uncomfortable thing is that this can cut both ways. Things can and do get rejected because it doesn't fit the ideology.

Feynman called it Cargo Cult science:

    We have learned a lot from experience about how to handle some of the ways
    we fool ourselves. One example: Millikan measured the charge on an electron
    by an experiment with falling oil drops, and got an answer which we now know
    not to be quite right. It's a little bit off, because he had the incorrect value
    for the viscosity of air. It's interesting to look at the history of measurements
    of the charge of the electron, after Millikan. If you plot them as a function of
    time, you find that one is a little bigger than Millikan's, and the next one's a
    little bit bigger than that, and the next one's a little bit bigger than that,
    until finally they settle down to a number which is higher.

    Why didn't they discover that the new number was higher right away? It's a thing
    that scientists are ashamed of--this history--because it's apparent that people
    did things like this: When they got a number that was too high above Millikan's,
    they thought something must be wrong--and they would look for and find a reason
    why something might be wrong. When they got a number closer to Millikan's value
    they didn't look so hard. And so they eliminated the numbers that were too far
    off, and did other things like that. We've learned those tricks nowadays, and now
    we don't have that kind of a disease.

    But this long history of learning how not to fool ourselves--of having utter
    scientific integrity--is, I'm sorry to say, something that we haven't specifically
    included in any particular course that I know of. We just hope you've caught on by osmosis.

As you say, it takes a lot of faith to believe that we're now clearly on the path where the truth can only go one way. For example, given that history will always be discriminatory, is there a situation where it will be clear that societal discrimination now reversed to be against, say, white men? After all, even if it was in some hypothetical future, people could still point to history as a justification for why women or other races are actually the oppressed (it's essentially the argument you just made, I don't see why it'd be any less valid in 50 years or whatever).