Honestly, a lot of my memory of the manga has faded now since I haven’t been revisiting it or discussing it in a few years, so I can’t dissect it as much as you might be looking for. That being said, if you’re just looking for my opinion, my opinion is still that Kaname had no reason to punish Yuuki. But hear me out: when I say he had no reason, I mean that in my opinion he had no good reason or justification for his actions. Fiction or not, to me there is no justification for punishing someone you’re in a relationship with. It’s unhealthy, and can lead to abusive dynamics in a relationship.
Yuuki saying that she was okay with being punished doesn’t make it okay, because Yuuki was in a very unhealthy mental space when she said this. What she needed was emotional support, which Kaname was unable to give her because he wasn't in any better shape than she was. So for me, that reason has never been enough and if anything actually makes it worse. It just shows how unhealthy their relationship had become by that point.
Did Kaname feel his actions were justified at the time? Of course he did! And fans who sympathize more with him than Yuuki may even agree with him, because he has infinitely more experience in what she was hoping to do to change the world, and he has seen it fail time and time again. Even I can understand where he was coming from. But even if Yuuki’s actions were doomed to fail, that was her choice to make, because she deserved to have her own agency to make her own mistakes and learn from them.
That’s just how I’ve always felt about it, and always will, but I respect anyone who feels differently. It’s a series with a lot of unhealthy relationships and a lot of characters suffering from extremely poor mental health (re: suicidal tendencies), so it’s not like any of them really escape criticism when you look at their actions under a microscope. It’s a lot of why I’ve lost interest in the series, because I’m just not really interested in stories like that where there’s like... no light at all.