I came accross this website with some great extracts from R’ Chaim Hirschensohn (see here for more details) regarding a fundamental topic, that is paramount to any discussion pertaining to Orthodox Judaism. I think his response is refreshing, truthful and loyal to the spirit of Judaism, a religion focused on seeking the truth – wherever it may be found.
(Below is a copy of the extracts from the above mentioned site)
Our Sages of blessed memory have said: “Wise ones, be cautious with your words.” For a hareidi Rabbi visited me and was astonished to see that His Torah Honor [Rabbi Hirschensohn] writes in page 76 of his work contrary to the opinion of Rashi and the Tosafot, and that they [Rashi and Tosafot ] forgot or never knew what had happened in a certain historical instance. The Rabbi who was visiting said, “He must count seven clean days [on account of the impurity of the words].” I showed him that which the Rosh [Rabbeinu Asher, one of the Rishonim] wrote, that concerning the Torah, which is “truth,” one must not show deference to any man. Just as by the honor and fear that must be accorded by a son to his father, there are certain cases where a son may differ with his father. And Maimonides wrote in several instances, “my father and teacher is among those who forbid, while I am among those who permit.” Similarly, Rabbeinu Yaakov Baal HaTurim ruled in several cases contrary to his father the Rosh. However, I ask you to please formulate a proper response to his claim.
From a letter to Rabbi Hirschensohn by Rabbi Yechiel Michal Goldberg 2 Tamuz 5681  Malki Bakodesh IV, 30
…Regarding that which His Torah Honor wrote about a “rabbi of the hareidim” who visited him: Are there then any rabbis in Poland who are not “hareid” (fearful) of the word/Halakhah of G-d? Has Poland also become sick like Austria, Germany, and America, with “rabbis” of all different types? Undoubtedly, you must have meant by the term “hareidi” one whose fear of sin precedes his wisdom; and even though our Sages of blessed memory have promised that the wisdom of such a man “endures,” they did not promise that it would grow or expand. Wisdom that was not acquired by virtue of hard work and study will not be helped by the fear of sin.
Rashi and Tosafot – indeed, all of the Rishonim – are holy and precious in our eyes; “the earlier ones [lit., rishonim] are as angels.” However, no matter how great a man is, whom “G-d has made a little lower than angels,” he is still mortal in that he cannot know more than he has seen or heard or studied. Even a giant in Torah, if he has not done one of these three things, cannot know something, if not by way of prophecy – which has been removed even from prophets ever since the destruction of the Holy Temple. And even during the days of the Second Temple, it is told (Horayot 10a) that Rabbi Joshua knew that there was a certain star that appeared once every 70 years that could cause ships to go astray, and so he took extra food along on his ocean journey, while Rabban Gamliel did not know about the star. Should this be considered a slur or offense to Rabban Gamliel, who was a great astronomer and who even had a scheme of the moon laid out in his attic? It is also related in the Mishnah (B’chorot 4) that Rabbi Tarfon did not know that cows were not exported from Alexandria with their wombs intact, and that if a certain Dr. Todos had not taught this fact to the rabbis, it would not have been known. Many other such examples of this can be found in the Talmud and Medrash.
If Rashi and Tosafot never read Roman history, and did not know that before Hadrian built Aelia Capitolina upon the ruins of Jerusalem, the wall of the city was simply breached and not totally razed, and that Jews even lived there – this is not a slight at their honor, for they could not have known these facts without having read the history books of the nations. And if, by virtue of knowledge of these facts, a Talmudic passage can be explained differently than the way Rashi and Tosafot explained it, this is the honor of Torah, and not, Heaven forbid, an insult at these earthly angels of G-d. Just as it is not an insult to Rabbi Tarfon and the other rabbis, who would have ruled many animals “unkosher” had not Dr. Todos come along and taught them.
Regarding the concept of dispute with the Rishonim, whose seal is truth, I have already quoted the words of the Rosh (in Malki Bakodesh II, p. 85), and every upright man will concede the truth of this point. The Rishonim themselves will rejoice in their Heavenly paradise over the fact that from their words comes the Halakhah, and that the truth will be established forever.
From a response to Rabbi Y.M. Goldberg Malki Bakodesh IV, 33
The axis revolves here around the matter of issur (forbidden) and heter (permitted). If it were to be forbidden for later authorities to rely upon their own thoughts and intelligence against the opinion of the earlier authorities, then there would be no difference between issur and heter, for the main issue here is the power of the intellect, understanding, and logic.
Being that the Torah has granted the later authorities the right to reason and deliberate, even only to forbid that which the Rishonim permitted, we may rely on this power also to permit that which the earlier ones forbade, in the case where a later authority has reached, after careful study, what he considers to be the true Torah conclusion. He is then obligated, or at least permitted, to act according to his conclusion, even if it is contrary to that of the Rishonim, as I have explained in Malki Bakodesh II, p. 85, and in a footnote on p. 86; I quoted the Rosh, who said (Sanhedrin IV, par. 6), “Everything whose law was not presented conclusively in the Talmud, one may build up and tear down, and even differ with the rulings of the Geonim.” See also Vol. IV of Malki Bakodesh, p. 64, and see my response to Letter 13, and p. 67, and other passages there. The chief proof of my point is from Hezekiah, about whom it was said that he knew something that those who preceded him did not – not because of their ignorance, but rather because G-d decided that Hezekiah should merit this knowledge. It is not haughtiness [on the part of those who claim to know], but this is rather the natural way: when a matter arises in practice, those who must deal with it learn new aspects that those who preceded them – who did not have to deal practically with the issue – never had a need to know other than in their academic studies. I wrote a similar point concerning Beit She’an.
From a letter to Rabbi Yosef Ben-Tzion Baavad 6 Kislev 5684 (1923) Malki Bakodesh VI, p. 111