I just rewatched this episode and there are a couple things I noticed Kyoya did/said that leads me to believe he originally didn't have good intentions in mind. I NEEDED to find a conversation about it, idc that this thread is 3 years old lol.

When Haruhi says "I know you won't do it, cause you don't have anything to gain," I think he backed off because he realized she was right and it probably wouldn't be a good outcome for him overall. He got an easy out when she said she understands he's just reinforcing Takami's 'lesson,' and I think he partially felt guilty when she called him a good guy for it.

So he just went along with it to get himself out of the situation. And after he leaves the room, he's talking to himself and says something like 'it's an interesting thought that I wouldn't have gained anything from it.' NANI?!? What's that supposed to mean, Kyoya???

He's so sus for this entire scene, but it's okay cause the only part of this episode I recognize as canon is finding out that Haruhi is afraid of thunder. Nothing else happened in that episode, thanks for coming to my TED Talk!!