He mentions in the acknowledgments was because of Into Darkness so I'm guessing a Marcus mention perhaps? Can't think of anything else that would require the alterations.
At the beginning of STID, when Pike is brow-beating Kirk about letting the natives see the Enterprise when he rescued Spock (and possibly for preventing the volcanic eruption at all), Kirk defends his record by pointing out that not one member of the crew has been killed since he assumed command of the ship. It's a little obvious, knowing that restriction, that the Enterprise personnel that got attacked by the aliens in the book were originally written as having been killed, not rendered comatose, especially how in the last chapter there's just one quick line that McCoy figured out how to revive them all off-screen after the main action of the book had concluded.