[OBW]

Interesting questions. Some thoughts that came as I read your post:

The whole area was under the administration of Roman rulers who propped up locals to be part of the administration. There were also Roman soldiers and others living within the Jewish lands. There are even accounts of gentiles who were following, or who came to Jesus for healing for their servants, children, etc.

But despite the religious turmoil going on in the land during Jesus' ministry, it was not the Romans who sought to silence Jesus, but the Jews, or more specifically, the Jewish religious leaders. Even at the crucifixion, Pilot was only placating the Jews. He allowed it, but was not the driver of it.

While some may have made more sweeping things out of John's reference to it being the "Jews" who wanted to kill Jesus, it was not all of the Jews, but it was confined to members of that group (or there is no record to suggest otherwise of which I am aware).

In our politically correct world, we would expect that John write something like "the religious leaders of the Jewish religion, or at least a portion of them" so as to clarify that it was not all Jews who sought to kill Jesus. "The Romans" were occupying Judea, Samaria, and Galilee. But clearly not all Romans were. Neither did every Roman even know where Judea, Samaria and/or Galilee was.

"He came to his own and they rejected him." But his own were the bulk of his first followers and believers. Is John's comment more a confirmation that the prophecy that he would be rejected by the Jews in general was true than a comment about Jews? Does the nationality of those who sought his death capture all who are of that nationality?

I do not see how not being counted among the Jews that sought Jesus' death means that John did not consider himself a Jew. And I do not see anything that colors his understanding of Christianity as completely separate from Judaism. Jesus said he came to fulfill the law, not to tear it down. Judaism was not over, per se. It was completed. We call it Christianity.

And in that one change another prophecy became fulfilled. All the nations are now blessed.