Maybe I need to add an option so you can't choose an actual character name as the Hero's name!
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It could just be an option to rename the main character later during gameplay. That shouldn't be as demanding on the coding as giving the option to rename major characters. Or just add "The Other " to text mentions of the other character. That might be a bit silly though.
Also a warning pop up "There is already a character in the story with that name, are you sure?" confirmation could be another solution.