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Balofsky comments on Ontologial Reductionism and Invisible Dragons - Less Wrong Discussion
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-Regarding Maimonides, it should be noted that he considered such negative knowledge to be the product of positively acquired knowledge; it's the same as what I mentioned in the article on yedias hashelilah. This is why he cited 25 propositions from Aristotle in the Guide for the Perplexed, as supports for his negative theology.
-I cede your point about many rabbis not being pro-empirical; the Rabban Gamliel example is a good one. However, I'll add that very few Gaonim or Rishonim were willing to flatly deny clear empirical evidence, and were generally just fine admitting that many of the Talmud's scientific claims were incorrect. Also, I'm not aware of many rabbinic authorities who have poskened on halacha on the basis of non-empirical scientific claims.
Well, the most obvious pointer if you want an early thing are all the sections of the Talmud dealing with the female menstrual cycle.
More modern examples also exist. The Chofetz Chaim repeated the claim that lice spontaneously generate in the Mishnah Beruah as why one poskens that killing them is ok on Shabbat. He's only writing in the 1890s, 30 years after it was already conclusively established that spontaneous generation was wrong for microscopic organisms, and 200 hundred years after the scientific community had already established that it wasn't true for macroscopic organisms. This is only the most commonly used text for poskening halacha for all of Judaism today.