Also, were there critics who said "To hell with past works," since their personal views of the song conflicted with what music theory was telling them?
I think this is a bit of confirmation bias stemming from an entrenched, Romantic-era notion that genius artists are not understood by their contemporaries. While it is true that some compositions may have been poorly received in their day only to be re-evaluated by later generations, this is hardly a systematic problem. There doesn't seem to be much actual historical evidence that critics are routinely making the wrong calls when they evaluate works. Beethoven works like the 5th and 9th symphonies were famously well-received, with the 5th inspiring arguably one of the first landmark essays in music criticism by ETA Hoffmann. The famous "too many notes" quip from Amadeus is likely apocryphal, emerging in 1798 writings by Niemtschek, a full 7 years after Mozart's death! A testament to how early some of these romantic myths were established.
The composer that perhaps was the most systematically overlooked in his own day was J.S. Bach, but it was not because he was thought of as forward thinking. Quite the opposite! He was regarded as writing in a style that was by that time considered out of date. The cool kids were listening to opera, not chorales and keyboard fugues. And his sons, most notably CPE and JC Bach, did very well by writing in more up-to-date genres and keeping pace with the market.
All that is to say, there is very little historical evidence to support that critics systematically mis-judge the music of their day, or consistently bashed works that we treasure today. Of course, one can pick and choose such remarks and fashion such a narrative if you so wish, that's pretty much exactly what Amadeus did. And no doubt it sometimes did happen that way. But it seems fruitless to discuss from a general standpoint because I don't think it holds up at that level. But if you took a particular piece that seemed badly regarded by critics of the day and investage the individual circumstances surrounding that, then I think you'd be able to tell a cool story about that particular piece! But you'd have to find one that you are particularly interested in knowing about first!