In response to YEZ, Feb. 28:
The distinction made in Dynamics of Dispute (pages 125 and following) is not halacha vs. aggadta. It is between teachings by Tannaim (of whatever category) that definitely did not originate with Moses' report of G-d's explanation, and all others. Only the former are candidates for dispute. The Rambam certainly maintains that among those teachings, transmitted to and by the Tannaim (as well as Amoraim), are historical accounts and hashkafic ideas that he likewise accepted as fact. (For example, creation ex-nihilo, and the accounts of the Mabul, Avraham's miraculous escape from Nimrod, and the desert wanderings (see Moreh Nevuchim 3:50 and Hilchos Avoda Zorra 1:3)
The main source for the explanation for why Amoraim abstain from disagreeing with Tannaim (when they do) is a passage in the Talmud Yerushalmi on Payah 2:6:
Said Rebbi Zeyra in the name of Rebbi Yochonon: "If you come across a mishna whose reason you cannot understand, do not brush it aside and replace its law with another one. For many laws were told to Moses at Sinai, and all of them are lodged throughout the Mishna."
Said Rebbi Abbin: "How true! For behold the halacha regarding "two varieties of one grain"[as a prime example]! If Nachum HaLavlar had not come and explained to us [that it was a halacha L'Moshe MiSinai], would we ever have known?!"
From this source, one deduces that immediately following the formulation of the Mishna—the time of Rebbi Yochonon, at the beginning of the era of the Amoraim (c. 4000, 250 CE), the tumultuous state of affairs caused an obscurity over which laws had originated with drashos, permitting challenge, and which laws had really originated from Sinai, precluding question.
As summarized in the final paragraph of that chapter,
All details in the Mishna known not to be kabballos, and all
rabbinical decrees not yet voted upon by a Tannaitic Sanhedrin, were
challengeable. On such issues, an Amora could conceivably differ
with a Tanna. As we mentioned above, there were rare instances in
which Amoraim exercised this power.