I could probably mount a plausible argument that the end-game is to discourage talented developers/cryptographers from contributing to the sorts of projects that could be seen as "sticking it to the man". Especially since this isn't a singular isolated anecdotal story (and I know the plural of "anecdote" isn't "data", but still…)
If making that argument (and I'm not yet sure I'm convinced of it's "rightness"), I'd probably also point out it doesn't need to be on the scale of "the United States government" to exist or to be effective - it could be emergent behaviour of law enforcement agencies without being publicly chosen or acknowledged policy. A diligent "national security" agent might very well think it's entirely within their remit to "investigate" software like CryptoCat, and the Chinese Whispers propagation of that "I wonder what algorithms CryptoCat uses?" curiosity could easily end up with the observed "The NSA needs to know about your software" interrogation/intimidation behaviour by the minimum wage airport security staff.
And as a long term play - putting even a little pressure on young up-and-coming developers when they're deciding what projects to start or contribute too would "work". "Should I contribute to this borderline subversive open source crypto project? But what if I get a startup off the ground later that requires a lot of travel? Maybe I should work on my commercial mobile app idea instead…"