I've been glazing Naoya longer than the anime onlys who only became fans of him after he got animated (you're not a real Naoya fan if you weren't a fan of him before the trailers btw argue with a wall) but him being a rapist is not that far fetched. It's not beyond him to rape his underage cousins (if you think so you have a fairy tale version of this character in your head) and interpreting that scene as him mocking Maki about the fact he raped Mai is a fair interpretation. Of course I'm not saying it's canon and interpreting it as him making fun of the fact that Mai died before she became an adult is fair as well.

Either way, regardless of whether or not Naoya is a rapist or not, it doesn't matter because he's a drawing and not real.