You know this is the script born in the Dev's head and embodied in the game, right? This is the original idea that has been gradually leading us to a future threesome storyline there. Well, as in life, the past cannot be changed or cut out of your life (of course, you can erase things from your mind, but that's a completely different issue). It's an experience happened. BUT as for the gameplay...
At the moment, there's a little 'artifice' that allows your MC to be kept in the dark about their past relationship. You just need to reject Yuki since it's tied to her character, in particular. So, you won't see that scene in their room, then them arguing in the hallway and all futher events with Yuki giving more and more opportunities for him (holding the info) to get closer to her. And thus it won't be recorded in both Yuki and Carol's bios. Of course, you can't unsee what you've seen, but it's the only way around it.
That's how it works. Hopefully, if there won't be any Yuki's content in the story, it won't trigger your Carol to share those juicy details from her and Yuki's past with your MC
It would make sense in the game reality. Carol simply wouldn't have had a reason to start a conversation on this topic, and the MC wouldn't have had a thought to ask about it. And even if his loving Carol, who always tells him truth and doesn't conceal any secrets from him, would have still wanted to share this with the MC, this would have been a (pleasant?) surprise for him and would have remained just a fact from her bio. And it wouldn't have turned into something more and wouldn't have affected their further love relationship.
