They did predict it- they made a rule ahead of time to make sure they retained control over the name in such an event.

They sent a spokesman on the Colbert Report to play along with Stephen even as they got the word out about the space station. All Stephen's viewers, anyone reading news reports about this "controversy," and everyone in this thread, are all learning about the ISS as well. I'd say NASA has made it work for them quite nicely.

I don't think the distinction between the people voting for Serenity and Colbert is as sharp as you suggest. "Serenity" was the the name of the ship from Joss Whedon's Firefly TV show and Serenity movie, and his fans conducted an organizing voting campaign of their own. At any rate Stephen is a huge science/NASA geek and an all-around mensch, so I'm certain he's going to be thrilled no matter what NASA decides to do even as "Stephen" throws his outrage around like a monkey's feces. Check out this episode to see the real Stephen's love of space travel seep into his interview with an astronaut on the ISS. Personally, Joss and Stephen are perhaps my two favorite television types ever, so I'm also happy with the outcome, whatever it may be.