Q:

Rambam and Chazal

In his letter to Chachmei Luniel, Rambam says that the belief in astrology was a minority view in chazal and we should not follow it. 

...it is not proper to abandon matters of reason that have already
  been verified by proofs, shake loose of them, and depend on the words
  of a single one of the sages from whom possibly the matter was hidden
  (Isadore Twersky Translation)

In Moreh 2:26, he admits it is possible some sages(Pirkei Dirabi Eliezer) held like Plato, even though he thinks such an opinion is very wrong.
What are other examples of him specifically saying an opinion he finds to be abhorrent was held by a minority in Chazal?

A:

In Guide for the Perplexed 3:48 Rambam identifies the opinion of a Mishnah (at least according to one interpretation in the Talmud) as being one of two philosophical opinions he discussed earlier:

When in the Talmud (Ber. p. 33b) those are blamed who use in their prayer the phrase, "Thy mercy extendeth to young birds," it is the expression of the one of the two opinions mentioned by us, namely, that the precepts of the Law have no other reason but the Divine will. We follow the other opinion.
(Friedlander translation)

If we look back at that discussion in Guide for the Perplexed 2:26 we see the two opinions:

As Theologians are divided on the question whether the actions of God are the result of His wisdom, or only of His will without being intended for any purpose whatever, so they are also divided as regards the object of the commandments which God gave us. Some of them hold that the commandments have no object at all; and are only dictated by the win of God. Others are of opinion that all commandments and prohibitions are dictated by His wisdom and serve a certain aim; consequently there is a reason for each one of the precepts: they are enjoined because they are useful.
(Friedlander translation)

In Guide for the Perplexed 3:31 he reveals the abhorrent nature of the second opinion:

THERE are persons who find it difficult to give a reason for any of the commandments, and consider it right to assume that the commandments and prohibitions have no rational basis whatever. They are led to adopt this theory by a certain disease in their soul, the existence of which they perceive, but which they are unable to discuss or to describe. For they imagine that these precepts, if they were useful in any respect, and were commanded because of their usefulness, would seem to originate in the thought and reason of some intelligent being. But as things which are not objects of reason and serve no purpose, they would undoubtedly be attributed to God, because no thought of man could have produced them. According to the theory of those weak-minded persons, man is more perfect than his Creator.
(Friedlander translation, my emphasis)

(Though it exceeds the scope of this question/answer, it is worth noting that Rambam in other writings seems to accept the very view he decries here.)
Another instance in which he asserts that a minority of Chazal was wrong on a fundamental theological matter (though perhaps not abhorrently so) is in Guide for the Perplexed 2:29. There he writes:

Our opinion, in support of which we have quoted these passages, is clearly established, namely, that no prophet or sage has ever announced the destruction of the Universe, or a change of its present condition, or a permanent change of any of its properties. When our Sages say, "The world remains six thousand years, and one thousand years it will be waste," they do not mean a complete cessation of existing things; the phrase "one thousand years it will be waste" distinctly shows that time will continue: besides, this is the individual opinion of one Rabbi, and in accordance with one particular theory. But on the other hand the words, "There is nothing new under the sun" (Eccles. i. 9), in the sense that no new creation takes place in any way and under any circumstances, express the general opinion of our Sages, and include a principle which every one of the doctors of the Mishnah and the Talmud recognises and makes use of in his arguments.
(Friedlander translation, my emphasis)

A similar example occurs with another fundamental matter of theology in Guide for the Perplexed 3:17. He writes:

We, however, believe that all these human affairs are managed with justice; far be it from God to do wrong, to punish any one unless the punishment is necessary and merited. It is distinctly stated in the Law, that all is done in accordance with justice; and the words of our Sages generally express the same idea. They clearly say: "There is no death without sin, no sufferings without transgression." (B. T. Shabbath, 55a.) Again, "The deserts of an are meted out to him in the same measure which he himself employs." (Mish. Sotah, i. 7.) These are the words of the Mishnah. Our Sages declare it wherever opportunity is given, that the idea of God necessarily implies justice; that He will reward the most pious for all their pure and upright actions, although no direct commandment was given them through a prophet; and that He will punish all the evil deeds of men, although they have not been prohibited by a prophet, if common sense warns against them, as e.g., injustice and violence. Thus our Sages say: "God does not deprive any being of the full reward [of its good deed]" (B. T. Pes. 118a) again, "He who says that God remits part of a punishment;, will be punished severely; He is long-suffering, but is sure to exact payment." (B. T. Baba K. 50a.) Another saying is this: "He who has received a commandment and acts accordingly is not like him who acts in the same manner without being commanded to do so" (B. T. Kidd. 31a); and it is distinctly added that he who does a good thing without being commanded, receives nevertheless his reward. The same principle is expressed in all sayings of our Sages. But they contain an additional doctrine which is not found in the Law; viz., the doctrine of "afflictions of love," as taught by some of our Sages. According to this doctrine it is possible that a person be afflicted without having previously committed any sin, in order that his future reward may be increased; a view which is held by the Mu’tazilites, but is not supported by any Scriptural text.
(Friedlander translation, my emphasis)

Note that in this case he not only rejects what he terms a minority view, he accepts instead a Talmudic opinion which the Talmud explicitly claims to have refuted!

