Answer

Hello Yonatan. Let me begin by saying that my opinion is certainly no more important than the opinion of the Talmud itself. So if one may rule against the Talmud, then one may certainly also rule against my opinion. Therefore my opinion is not really what matters here. What I can write is which considerations are worth taking into account when you come to make your own decision on the matter.
As a rule, we generally accept that one does not issue halakhic rulings against the Talmud. Therefore, ruling in light of an interpretation of a tannaitic source that goes against the Talmud is problematic. But this is a theoretical statement, since almost always you can force the reading a bit and find a conflicting passage or a Jerusalem Talmud, as halakhic decisors and medieval authorities (Rishonim) have always done. I would definitely understand someone who did so in a case where it is clear that the Talmud missed the intent of the Mishnah or the Tosefta.
Interpreting an amora against the anonymous Talmudic layer is easier, because here there is no direct departure from the Talmud, although here too, if the anonymous layer interprets the amora, one could say that according to the Talmud there is no such opinion on which you could base a ruling.
More generally, I would say that the rules of halakhic decision-making are usually a basis for exceptions. Already the medieval authorities (Rishonim) deviated from them more than once, and I suspect that from time to time they did so because they decided that the opinion that should have been ruled upon was less reasonable. In general, one should treat the Talmudic rules with caution, as the Talmud itself hints more than once (there is a certain dismissiveness toward rules, and I think you’ve already heard that from me).
Therefore, everything I have said here has rather limited significance. In the end, it seems to me that every sweeping statement comes with reservations. Everything depends on how convinced you are by the conclusions of academic research—that is, that a mistake was made in the traditional interpretation—and how problematic/necessary the ruling is. If you are very convinced, there is much more room for halakhic creativity, and so on.
 
I will add just one example. Years ago I read the book of my friend Professor Berachyahu Lifshitz on asmakhta. I was persuaded by his main claim that the accepted interpretation of the concept of asmakhta is mistaken. Originally it was interpreted one way, and following Maimonides all the medieval authorities (Rishonim) and halakhic decisors tended to interpret the term differently. After reading it, we discussed a bit what should now be done in practice. I myself am very torn about this, but nowadays my view tends toward ruling in accordance with the original meaning. The reason is that here the change took place after the Talmud, and Maimonides does not have authority comparable to that of the Talmud. Therefore here one should follow the truth. By contrast, if the Talmud itself erred, that is the meaning of authority—that one follows it even when it erred. However, nowadays I am less convinced that Berachyahu is right, and this is not the place to elaborate.
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Questioner:
 
Let us take the last example, regarding Maimonides’ interpretation of the term asmakhta as opposed to the original meaning of the term. In this case, it was Maimonides who innovated the meaning adopted by the medieval authorities (Rishonim) who came after him, but it is possible that the Geonim or earlier medieval authorities interpreted it differently.
What would you say in a case where so-and-so (a scholar or rabbi) proposes a new interpretation in the Talmud—not against the anonymous Talmudic layer, but against all the medieval authorities (Rishonim)? Would you also say then that it is easier to disagree and rule differently? Does the fact that all the halakhic decisors understood the passage in a certain way carry weight (beyond increasing the likelihood that the new interpretation is mistaken)?
Yonatan
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Rabbi:
I would say the same thing as regarding asmakhta. It carries weight, but it is certainly not absolute.