Kudos to JJ Abrams and crew for realizing this joke had to go.
Deleted scenes offer a window into the filmmaker's minds; you can look at what they were playing with as they approached the final edit, get a sense of their intentions but also what they discovered as they went along. Many films truly take shape in the editing room, and scenes that looked to be slamdunks get left on the floor. The editing room also allows a filmmaker to modulate things - to hit a point more softly, perhaps.
This Star Trek Into Darkness deleted scene shows Captain Kirk making his false log report about the action at Nbiru; a Star Trek nerd friend sent it to me angrily and at first I didn't get what the big deal was. I like how Pine delivers the log entry. Then I got to the end, and I was floored. The clip has the entire bridge crew of the Enterprise looking at Kirk - who has just finished lying on an official record - and basically rolling their eyes and gasping in horror. His reaction boils down to 'What's the big deal?'
It's a horrible moment, one that profoundly undercuts James T. Kirk not just as a man, but also as a leader. There's no way anyone on that bridge would take this idiot seriously again. It's hard to imagine any of these characters scraping together enough respect to follow his orders in the future. The idea that the filmmakers thought Kirk should not only lie like that in front of his whole crew but also give them an incredulous 'Whaddya want from me?!' reply points to the cancer that is eating away the heart of the rebooted Star Trek films. Even murderous Mirror Universe James Kirk wouldn't act like this.
Thankfully it was cut from the film. Star Trek Into Darkness is already a bad movie and a worse Star Trek movie; this scene would have poisoned everything. Whoever made the choice to cut it was right. Whoever made the choice to even get so far as filming it should be forcibly removed from the 23rd century.
Interestingly the fact that Paramount spread the STID special features across multiple platforms means my hardcore - and I mean hardcore - Trekkie friend only just saw this clip this week. What other gems are hiding out there?