The names of my nephew and my aunt have a homophonic sound.

There is no need to change it. The pronunciation is different and the words are different. The homophones are not considered homophonic, they are just similar. They don't live together, and my sister is no longer here, so there is nothing to worry about or taboo about. If you just can't make it, go to the police station and change your son's name. That's it, it's not complicated.