It is on the person who makes the objection to prove that the Jews of Medina did not believe in this concept as the Jews of Medina were addressed specifically in a part of the verse.
The discussion in the context is not Ezra but something else.
You may take help, if you like, from Jewish friends in the forum or from elsewhere with whom the issue concerns directly.
They should prove that Jews of Medina did never have this concept.
Jews were divided in sects and denominations; this trend continued. New sects/denominations emerge and the old ones vanish.
Quran is not a book of history. Quran deals ethical,moral and spiritual issues in a reasonable and pragmatic way.
Regards
I would agree with you, yes, that when a person seems to have a plausible theory, the way to discredit it, is by disproving it.
However, your claim is that when the Jews migrated to Medina, they merged with other denominations they maintained a belief completely foreign to Judaism.
The first problem is that if the Jews merged with their pagan neighbors, then within just a few short generations, you wouldn't have any more Jews just pagans.
The second problem, is that historically Jews don't seem to intermarry, which has made us especially valuable for genetic studies. So you're working against a trend here.
The third problem is suggesting that Jews running from Christians, would take a belief that is congruent with Christians just in a Jewish framework.
The fourth problem is that you want to say that the Jews adapted pagan beliefs, but the specific belief that is claiming to have been adapted doesn't seem to be found among any pagan tribes of the neighborhood. It is (according to the claim) specific to Jews and not pagans.
The fifth problem is that its more likely that a non-Jew should be mistaken about Jewish beliefs, then that an entire sect of Jews should change their beliefs.
Taken altogether, what you have here is an extraordinary claim. And when it comes to extraordinary claims, you don't say that the onus is on the disbeliever to disprove it. You say, that the believer has to provide extraordinary evidence.