In my WIP, both Chiron and Charon are minor characters. I was thinking of changing Chiron's name to "Kheiron" to make it less confusing. I thought about using an alternate spelling for Charon, but he's the more well known of the two, though my depiction of him is a little different than most people imagine him, so I thought I'd use his more common name. I'd personally prefer to just use Chiron and Charon, but I think it will be hard for people not used to those names to follow.
Why not give Chiron a nickname? With that, you can clarify to both the audience and any character in your story of the confusion (if there is any) and not worry about the audience mixing up the two. In addition, you mention both characters are minor, so take my advice as you will