By the time the conversation had ended, I had decided I needed to do some research to ensure what I was doing was in fact ok. I e-mailed my dad to ask him if the Rabbi had a source, and also picked up Rabbi Dobrinsky's excellent A Treasury of Sephardic Laws and Customs. After going back and forth, I realized that I needed to change my minhag. When I told my dad this, he approved but made the following comment:
Unfortunately, the people who say that the tradition is untenable if there is no source are cementing the Holocaust’s work, because these communities’ written halachot were destroyed in the holocaust.
It hurt me to read that. I'm extremely proud of my roots, and do my best to adhere to customs that have been passed along for generations. It left me in a bind.
This morning after shacharit, I had a long discussion with Yossi, who reads the Torah every Shabbat morning. I told him why I was struggling with what to do. He made the point that since the minhag does in fact clash with the halacha, it's best I do change the minhag. However, he then stressed something that I was foolishly overlooking. I can still teach Nissim that this was done in Rhodes (even if we do not practice it in Israel) while actually teaching and observing with him the Rhodesli customs (with regards to food, nusach and music for example) that were passed on to me by my parents.
I hope that, like my father & mother with me, I'm successful in transmitting my enthusiasm, love and appreciation of these customs* to Nissim (and G-d willng, the other children that follow) so that he carriers them, like me, on his journeys.
* I'd just like to add that while these customs are important, they're 2nd fiddle to teaching Nissim to love his faith and be an active & respectful member of Am Yisrael.