Update on this one: I finally hit the equivalent scene based on the route I was on (I'm currently on the Aomi-san route where I will end up with her by the end), and I don't think the Anime could have done much better, not because it was bad. The original Visual Novel handled it in a way that only an interactive medium could: every scene that lead to it required commitment from the player. I think the Anime really should have just axed it completely because of how much the game built up to it and prepared the player for it.
Spoilers below this line
The VN still dropped it directly on the player in a way that could shock those that weren't paying attention but it completely stopped the music and sound to convey it. It also didn't make the Keitoku's plight just an explicitly bad thing. It directly commented on how the system was flawed but wasn't inherently evil. The alternatives that seemed like they could be better and right were also just as bad in other ways, which was not something the Anime even attempted to discuss. I need to play the other routes to see what the differences were but I'm getting the impression that there might be a bit of legitimacy to playing all of the routes to get the full story. (could just be minor changes like some girl flashing the player her panties or something less fulfilling; I hope this isn't the case).