I've run across a number of instances on various discussion boards of people saying that you can see him almost smiling, and on that "under penalty of court martial..." line I think they're right. I do hope the take with Quinto being surprised by Pegg's ad lib makes it into the gag reel -- I'd love to see that.I just dug that trailer up again. When you go to the official st site, and go to trailers, its the one titled "answer me"-- after Pegg says his line, it really does look like Quinto is on the brink. Of course, i probably wouldnt think that had they not told us in interviews how hard it was to do that scene with a straight face! OR perhaps, that was the most serious take they could get!

Edit:
That trailer/video clip can be found here, about halfway down.