Regarding your claims (i.e. it is permissible for you (!) or your rebbeim to argue with a Tanna or Amora)... Surely you are aware that each generation (i.e. Tannaim, Amoroim, Rishonim, Achonim) could not argue with an earlier generation category (i.e. an Achron can't argue on a Rishon)! This is a basic fundamental point. Otherwise why the whole idea of diffenret generational categories?? I don't see how you can make the claims you are asserting earlier in the thread. Even an Amora cannot argue on a Tanna. And you claim YOU [or even your rebbeim] can!?
The Gemara will often attempt to disprove the statement of an Amora from a Mishnah, Beraisa, or Tosefta. If no other Tana is known to share the opinion of the Amora, the Gemara will either explain the statement of either the Tana or Amora in such a way that they are not contradictory, or it will conclude that the opinion of the Amora has been disproved.
One of the rules upon which Talmudic discussion is based is that the words of the amora'im must always be in agreement with the teachings of the tanna'im. Thus, one of the most common questions found in the Gemara is "meisivei" - which brings a tanna'itic source like a Mishnah, baraisa or tosefta that seems to contradict the words of the amora. In his defense, the amora will have to explain how the statement of the tanna can be understood as being in agreement with his own, or else show that there is another tanna with whom the amora agrees. If the amora cannot reconcile his statement with the teaching of the tanna'im, the Gemara will conclude "teyuvta" - the statement is disproved.
The Mechaber in Kesef Mishna, Hilchos Mamrim 2:1 writes:
Amorim can't dispute Tannaim, and later generations can't dispute Amorim because the Amorim accepted the authority of the Tannaim, and the later generations accepted the authority of the Tannaim.
The Chazon Ish says that such acceptance is an acknowledgement that the earlier generations are more correct since they are wiser and closer to Sinai. (Chazon Ish, Letters 2:24) And the Maharal (Beer Hagolah 6) says that the Amoraim recognized their inferior state in relationship to the Tannaim and therefore didn't argue with them.
In Choshen Mishpat, siman 25, there is a lengthy discussion concerning to'eh bid'var mishna. While the general thrust of the halacha concerns dayanim and situations where their piskey din can be overturned, it does shed light on our issue as well, since the assumption about a d'var mishna is that it is something than we (at whatever generation the reader find himself) may not argue against.
Mishna and gemara are accepted by all to be d'var mishna - meaning explicit piskey din in these texts ( dinim hamefurashim ). The Mechaber adds divrey haposkim. The Nos'ey Keylim have differing views as to what constitutes "haposkim". The Mechaber, for obvious reasons, did not include himself; however, later authorities do include him. For B'ney Ashkenaz, the Rama is included. Later authorities add the Shach and S'ma.
What we see from all of this, and the nos'ey keylim as well, is that there are many areas where we do not accept disagreement, and if someone does disagree, that position is rejected.
However, we also see, that in areas where there is no clear consensus, one has latitude to disagree.
One last point: There is a discussion in the Rama about an unresolved machlokes and how to decide. Rama says that one may not choose to follow the "katan" against the "gadol", rather follow the one who is "gadol b'chochma u-b'minyan", with minyan defined as the one who has the most followers ( see S'ma 18 ).
And of course do not forget what Rav Zera says in the name of Rava bar Zimona in Shabbos 112b.