Much of Trek requires at least some mental gymnastics to make sense.
I know that and every other film and movie in existence requires mental gymnastics but that is understandable as it ain't reality, but Star Trek Into Darkness takes this into whole new extremes to the point where it becomes really really distracting, really really obvious and really really annoying.
It's up there (and goes beyond) with Sisko committing attempted genocide on those Maquis worlds, Picard and the crew just watching as a planet's atmosphere burns and kills the inhabitants while doing nothing about it! So Star Trek has had its muddled moments and occasionally totally destroys its characters with badly thought-out plots and episodes. But STID goes one step further.