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.
I've always thought the scream was 100% warranted. Kirk had just had his ship attacked, witnessed many deaths and injuries on his ship, a close friend of his lose a relative, had to take down a load of corpses that had their throats slit, see a fellow starfleet officer kill someone with a phaser before committing suicide, and see another close friend go crazy before a rather unpleasant creature emerges from his ear. And had his own son come at him with a knife.
Then the guy responsible for all mayhem this taunts him about it in a rather sneering fashion just to rub his nose in it.
Enterprise not as damaged as he's letting on or not, I'd be pretty fucking pissed at this dude by now