Sam, if you think it is not a silly question in its own right then the title can go to you.
Most Rishonim who give different interpretations from Chazal do so in the form of explaning the Pshuto Shel Mikra. There are Parshanim Rishonim who took the liberty to argue on non-Halachic Midrashim. The idea is that while Chazal were Mekabel the Torah, the Drushim are open game.
Anyhow, as I pointed out, rationalist then is not rationalist now. What we call rationalist are actually naturists. Rationalist means someone who weighs heavily on the rational mind. The Rambam had no problem with a Ness in the Torah. He didn’t try to explain the natural causes for the Makkos or Yosef’s psychoanalysis. But he disagreed with the world categories being blurred.
Most Gemaros about extra fantastic events are also usually translated to something more nuetral. This is not a rejection of Nissim, but a rational understanding that such things are very uncommon, and that it is not even being portrayed as something so strange.