I think you bring up really good questions, and I'm sure that they are being addressed by those who study it. The main thing that's important about this research is that it shows that there is an undeniable link between refined sugar consumption and type II diabetes; I think that most earlier studies had similar conclusions but always left too many unanswered questions. This one appears to be very exhaustive.

And to your point about fruit, the authors control for fruit intake, which due to all of the good stuff in fruits is considered a positive by most doctors, and conclude that the refined sugar is the problem. Also, for comparison, a can of Coke has 39g of sugar, while an apple has 3g. So even if the sugars are equal, one would have to consume 13 apples to get the same effect.

This could be quite problematic for the corn syrup industry. In the past when companies are found to have been peddling a dangerous product, even in cases where the effects were unknown, they have been held civilly liable for their actions. Tobacco, asbestos, silicone implants, dioxin, and the list goes on and on. One wonders if diabetes patients can sue Yum, or Coke, or McDonald's for pain and suffering from their condition. Could be a huge can of worms, but hopefully it will get Congress talking about real, impactful changes to the farm bill.