
Can I say something with a bit of spoilers real quick?
1. He doesn’t rape him
2. He keeps him in a lab with all the necessary materials to do research that the government doesn’t let him do
3, the captivity only lasts a few chapters before plot happens
Also while I do admit saying “I can do anything I want with you” is a bit far. Showing him the rotting corpses was his way of telling Dr.Seok the rebels were full of shit. Heck I’d be mad too if someone I trusted started seeking out ppl that experimented on and killed all my comrades.
Also, since the government controlled the city, even if Dr.Seok did escape or if Major helped him escape, where would they go?? Okay yo another country maybe but then Major wouldn’t get away with that. He’s already betraying the second masters which will be shown in a few chapters

Spoilers pertaining to this comment.
Personally, while I agree with you said overall, he still threatenes to rape him. That he doesn't actually intend to do it or doesn't do so does not pertain to the matter at hand. As readers we have more information than Dr. Seok in that moment does, so he's thinking that Kwak actually will do that. They live in a different world, so we can't really 100% apply our way of thinking to them, but even if Kwak did it to protect him he's still traumatizing Dr. Seok. Both things can apply. Also Dr. Seok didn't know that garden of eden did experiments on people. I get why Kwak would be mad that Dr. Seok sought them out, but he didn't do it while knowing about the experimentations. I don't know what would've been the morally right way to handle this situation (not that people in any situation usually have the capacity to do so), but Kwak is definetly not a knight in shining armor (not saying that this is what you meant).
"He's doing this to protect Dr. Seok<3333" Yeah, I guess in a way. Like a bird in a cage is safe. Idk I feel like we shouldn't really ignore the brutality on display. There's a big difference between "Kwak puts on a show, that'd allow Seok to escape with his life" and "Kwak tries to traumatize him to the point, he'll never resist again". One views Seok as a person to help and the other as an object to keep. He didn't just threatened his life, he dragged him around and threw decomposing things at him and then threatened to rape him, because yes, that is what it was. Idk just acting like he's this poor victimized baby who has no other choice is pissing me off.