I am a former USMC ATC...part of that time stationed in Korea....I would guess that the controller did not want to broadcast the question "are you being hijacked" knowing that hijackers could be listening and then realizing that the pilots were hinting through comm with the ground that they were in trouble. periodically aircraft accidently squawk emergency codes such as 7500 and 7600....upon seeing that squawk a controllers phraseology is "Confirm squaking 7500"...due to the language barrier I'm not totally surprised that the pilot could misinterpret the question as an order. If he misunderstood he should have at least stated "roger we'll squak accordingly but we are not being hijacked do you still want us to change our transponder squawk?

The language barrier because more significant when in a crisis situation. As people panic and /or become more edgy their language proficiency declines...it was typical for Korean military pilots to discontinue speaking in English and start speaking Korean when faced with an inflight emergency even when they knew they were speaking to an American controller.