The problem with understand the story as one about God allowing the rabbis to decide Torah law, is that such an interpretation ignores several basic factors:
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the story takes place in the context of a sugiya about “ona’ah bedevarim”, fraud through words, especially, those who cause another public embarrasment.
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the story is a example of that happening – the rabbis humiliate R. Eliezer
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the proof text given that majority rules, actually says the opposite.
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R. Gamliel dies at the end of the story, proving the point: don’t humiliate someone in public, especially when all he is doing to trying to have the people follow God’s will in a given case.
The story is about rabbinic hubris, what happens when the rabbis do stop listening to God and think they can operate independently of God. Remember Baba Batra 12b: the holy spirit was taken from the prophets and given to the Sages. When the Sages stop listening to the ru’ach ha-kodesh (in the case the bat kol), their legitimacy is threatened.
I know how Eliezer Berkovitz and nearly every other rabbi interprets this passage (I have spoken to many of them about it), I show them that they start the story in the wrong place – you have to start at the beginning of the sugiya, not when the oven of Achnai is brought up. And, they it too early, with “nitzchuni banai”, instead going all the way to the end, and watching the rabbis wreak havoc, excommunicate R. Eliezer for no reason, and finally watch R. Eliezer call out to God, and then R. Gamliel dies.
God agrees with R. Eliezer; is not God the standard of right and wrong? Jewish law is not a system of conventional law, that whatever the court decides is the right law simply because court decides it. The rabbis have to attempt to accord their law with God’s will. Here, God made His will clearly known, and the rabbis disregarded it. R. Gamliel, the rabbi in charge, died for this.
The story is certainly not a simple story of rabbinic independence from God, but more likely, a story of the great perils and complexities of a legal system that is supposed to align itself with the Divine will.