My suggestion for understanding John's purpose for inclusion of the excommunication in
John 9 is to look not at the Birkat ha-mininm but rather to 3 John, where John writes about a
certain fellow named Diotrephes, who "loves to be first," who is excommunicating those in
the church who desire to follow the apostolic teaching. The point? This guy in the church (a
Gentile, I suppose) is acting just like those who had Jesus crucified. Thus it is actually an
anti-anti-Semitic message, by which I mean it shows the error of supposing the adversaries
of Jesus did what they did because they were Jews, as opposed to because they were human
beings. Jesus did not say "the Jews [uniquely] will hate you" but "the world will hate you."
Much of John's Gospel can be understood from the standpoint that John sees in the church in
its 2nd and 3rd generations, the same things he saw when Jesus ministered, teachers like
Nicodemus who know nothing of the need for the new birth, etc.