I think this is a lacking on the manhwa's part because Isabella didn't rape him it was actually mutual. His thought process during that scene in the novel was coherent enough for him to have angry sex with Ari's sister to cool down the fire or anger and denied pleasure be it physical or emotional from Ari. It was necessary as to show how despite the timeline change and the situations and circumstances being different, he's still a selfish person who ultimately cares more about how he feels and entitled enough to pull shit like that while justifying it with "I wasn't given what I wanted". It's not like Ari ever gave him hope that she'd accept him. His chasing was purely on his side, he knew she loved Alphonso, he knew she disliked him, and he knew she wasn't promising him anything. He just wanted her so bad that he thought he was entitled to her because he's putting in some effort, and once it was proven it won't change a thing he thought he's punishing her memory in his mind by having sex with Isabella, only to realize after that Isabella is crazy and this move was the worst he could've ever done because it made appealing to Ari almost impossible.
The manhwa portrayed him a bit differently that novel, making him seem nicer and so different from his first life that it's so painful to read and watch the manhwa version of him suffering this much when he obviously is purer than the novel version, that's why I can understand why you and many people (including me prior to reading the novel) felt bad for him in this timeline. I guess manhwa can't change major plot points, so it can't make things go nicer for him, that's why it seems like he's being judged for a life he didn't currently live. In the novel, he retains the same bad traits that even in his pursuit of Ari he's still exhibiting them.
In the novel, Cesare willingly slept with Isabella. I posted the excerpt here before. In the first place, didn’t he promise to stop drinking alcohol? Even if he was tipsy, his thoughts showed he was coherent enough to reject Isabella completely. In his thoughts, he was thinking Isabella doesn’t know how to kiss properly and he will teach her. For some reason, the WEBTOON changed this as they tried to whitewash his inner thoughts and paint Isabella as a lone actor.

Lowkey I only read this manhwa for Cesare. He started as a jerk who only took interest in Ariadne bc of Alfonso, but then slowly grow to care for her in his own way and tried to be a better person for her. Over and over Ari just pushed him away bc of the trauma from the first life. Then he got manipulated and raped by Isabella and dumped by Ari. Idk why the author bothered writing a sad traumatic back story for Cesare and showed him being abused as a child. Every time its shown that Cesare was just a product of toxic environment and could be redeemed, the author reverts back to punishing him for his first life behavior aka things that haven’t even happened yet in this life. Why put in so many chapters about Cesare or make the readers sympathize with him if they’re not going to go anywhere with his character? Putting the effort so he wasn’t just a one dimensional villain but then falling short every time by showing that his character never changed after all. Its just so dissatisfying and the plot is getting repetitive.