That's a fine take on the situation being glossed over, but I think it depends if you're part of the audience that cares more about the cozy slice of life feeling or a mature take on the subject. I was given scenes that tugged at my heart strings and seemed to give the "crew" something to bond over. Great. That feeling is all I want from the fiction. So to me, the situation succeeded in its purpose despite how it was swept away, but I understand we could have different perspectives. In that regard, I would be interested in an example of what you think would a more mature reaction.
I agree that Yuuhi is prejudicial based on what you said. I also agree it started as an undesirable part of his character. But I disagree that it necessarily makes him unlikable. This event spun his "prejudice" in a way that makes it an admirable quality. His bull-headed judgment that the girl wasn't completely malicious ended up saving the situation. More in his defense is that, frankly, hating someone for being better off and smarter than you is very relatable -- everyone experiences it; there's always someone better. Additionally, It's usually more fun to watch a not so great character learn than start with a saint character, like his friend, take over. In other words, is punching stupid? Yes. Have we all ever wanted to just punch someone in the face for being smug instead of being a mature adult? Yes. So, at this point in the story, I now see this as a chance for character growth over a reason to hate him.