R. Hershel Schachter on the prevalent forms of academic study of the Talmud (link):
There are individuals who consider themselves Orthodox who believe that at one time the Jewish people did have a Divine Torah, but the amoraim misunderstood the tannaim, the rishonim misunderstood the Talmud, and the achronim misunderstood the rishonim. “But don’t get me wrong,” they would say “– I’m Orthodox! And therefore I feel that the laws of the Shulchan Aruch are all binding, even though I think everything is in error.” This is not the Orthodox position. If one is really convinced that a certain psak is really in error, he is not permitted to follow it.
 It goes without saying that when evaluating a psak, one must factor in any discrepancy between his own knowledge and qualifications vs. those of the posek espousing the psak in question, and what such a discrepancy may indicate regarding which person is the one who is in error.