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I think that's the issue. Again, I'm no physicist, but as I understand it, the light is still moving at it's constant speed but the medium is basically making it move in a more circuitous route. So instead of exiting the medium at the shortest point, it's moving in an arc, or - in this case I think - a series of arcs. Maybe I don't understand the process well enough, but unless they're going to change the nature of a photon, it can't decelerate and then instantly accelerate once it reaches the exit. The fact that they're talking about it still traveling at C once it reaches the other end makes me think that it never slowed down, just took a very long route to get to the end.
Then again, I could be the one who has it wrong. At the end of the day, I suspect we'd need someone intimately familiar with the research to give us the right answer.
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