One of the things that was completely dropped, made no sense and had no point.
If it was completely dropped it wouldn't have been mentioned more than once as an ongoing concern of McCoy's, which it was.
It makes no sense to you that someone would suffer mental and physical trauma from being in the middle of a terrorist attack where several people were killed right in front of him, including his friend, mentor, adoptive father figure, the man who believed in and promoted him, his first commander, and his recent career savior?
It has no point in a film that's largely about shattering Kirk's overconfidence and false sense of immortality? Did you miss the whole speech shortly before the attack about how he had not lost any of his crew, and how Pike called him out for his hubris in thinking he's invincible? Did you miss Kirk's lack of confidence when Carol rebuffed his advances that had worked a thousand times before, including in this same film? Did you miss the utter anguish in Kirk's face later on when he couldn't think of a way out of the Vengeance destroying them, and his heartfelt apology to the crew? Did you miss Kirk's admitting to the fact that he didn't know what to do, he only knew what he could do? Did you miss his willingness to sacrifice himself for his crew as a result and his fear upon facing his own mortality?
Jesus, it's not like it was a hidden subplot or anything. The whole movie dealt with breaking down the self-made myth of James T. Kirk and making him into the more mature, responsible commander we knew him as in TOS.