I'm sorry, but this is a rather poor study. How can we tell? Most advocates of barefoot running would fully agree with the results, but from a very different perspective. Few, if any, barefoot running advocates would think that 10 weeks is enough time for one's body to recover from a lifetime of using modern shoes. In fact, the injuries described are exactly the kind that many of the more sober and realistic proponents predict for those who try to transition too quickly. They would simply say that this is evidence of how pervasive the impact of modern shoes on human abilities is. Moreover, Vibram FiveFingers represent the extreme end of the minimalist perspective in running, one that is controversial enough in its own right. (Besides, relying on Vibram's marketing spin is specious at best.) While some may regard FiveFingers as something to attain to, few would recommend it as a first step, and never in the way that the study was conducted. In other words, barefoot/minimalist advocates would agree with the study's results, but from a fundamentally different starting point and towards a fundamentally different goal.
Another way to say this is that this study was poorly designed enough to be entirely inconclusive, leaving those of us who make efforts to be data-driven to rely solely on anecdotal evidence. What would be far more effective would be a long-term, longitudinal study of minimalist style running that does not rely on methods even that community would regard as suspect.
In the end, all we are left with is fuel on the fire that produces smoke but little of substance.