Essentially, if Khan beams up Kirk then tortures and kills him the movie is over. So for three minutes they needed to change Khan's goal.
Call it what you will, but they wrote themselves into a corner.
Yeppers. Not only that they killed the impact of the scream and the "threat" by having Kirk know the whole time they had a way out.
And that's why Shatner's famous scream of Khan's name is made fun of. Not just for the cheesiness of it but the fact that it just makes no damn sense whatsoever.