Yes, the way I imagine most people will take this story is that Apple avoided taxes but really Ireland allowed them to contrive a tax structure that resulted in a lower tax bill. Apple must have known this would happen some day, I'd imagine they would have taken advice on it at the time and someone somewhere calculated that even if this happened, it was still worthwhile. So Apple isn't completely innocent but it's really Ireland at fault here.

There is no direct impact for Ireland e.g. a fine but it will create uncertainty for others already operating in Ireland and those considering investment. This uncertainty can be very bad for Ireland for years to come, so there will almost certainly be a penalty, albeit an indirect one.

Not quite. It's possible they'll feel the effect of the 1,000+ overseas companies with a presence in Ireland reassessing the pros and cons for their being there.

To whom should a country and its taxpayers be culpable in this situation? What would be the appropriate form of punishment?

WHAT the punishment would be could be a matter of discussion. My point was there SHOULD be some punishment. I can't imagine a case where Ireland walks out of this unscathed.

Their punishment, in this case, is having the EU step in and dictate what their tax laws should be, overriding Ireland's own tax laws.

To the European Union, I would think. Other European countries which are abiding to the rules are losing companies to those who countries offer unfair tax benefits.