Quite an interesting conversation happening here.
Lynn, it seems the rabbi of Anon's synagogue, like many rabbis, holds the belief that for a boy to be received as a member of the Jewish community, they must be circumcized. As the bar mitzvah marks the entry into Jewish adulthood, I suspect there were questions of how this boy would become a Jewish adult if he wasn't yet Jewish.
Many synagogues have rules concerning the way in which a family member or visitor to the congregation who is not Jewish may participate in services, whether or not they can receive honors (such as an aliyah), etc. (For more examples, you might look at our booklets,
Shabbat: What to Expect at a Synagogue and
Bar/Bat Mitzvah for the Interfaith Family.) It sounds like this rabbi may have believed this child was not Jewish. I hope that the family was involved in any decisions about the bar mitzvah. Perhaps they were asked to bring their son to a mikveh and/or a mohel/mohelet for a bris and declined. Perhaps the rabbi had creative suggestions on how to include an
"affirmation ceremony" as part of the bar mitzvah, but they weren't interested.
One of the complications that arises from changing or creating new rituals is that halakha (Jewish law) doesn't always keep up. It's possible that were this to happen again, it would be handled differently. But, depending on the Jewish denomination of the rabbi/synagogue, it might have a similar outcome today.