It’s a question of apikorsus. Those who said that chazal were mistaken were banned throughout the generations; that’s the “metzius.” Someone who has beliefs that are deemed apikorsus, even if based on Torah, are guilty of such. Their wine is assur, they lose their olam haba – it’s a pretty serious issue. And poskim are the ones who decide these things, such as the aruch hashulchan, the rabbonim who forbade the meor aynayim, and rav elyashiv, who forbade slifkins writings. They were quite familiar with the sources you brought; halacha doesn’t follow those opinions.
Instead, our job is to reconcile science with chazal, which is what gedolei yisroel have been doing for hundreds of years. Rav Belsky was a master of this, especially when it came to the places where chazal seem to be accepting spontaneous generation. What he said tied in an array of rishonim and gemaros.
But aside from apikorsus considerations, denying chazals statements has many other ramifications. Maybe their psychology was wrong, so we need to change אשה דייקה ומנסבה, אדם עשוי למשמש בכיסו בכל שעה, or hundreds of other psychological chazakos – the list goes on.