I am biased when I wished there was a fine, but there is not such fine, just collecting the owed money (and I don't know if with or without interest).
Apple followed the law that the Irish government presented to them. But Ireland, and Apple, are bound by EU law. I don't think you understand this, or at least you don't want to. Should Apple considers that the Irish government has lied to them, they are free to sue the Irish government (something they won't do anyways).
The EU does not control everything in the EU and lets governments decide many things, although within the frame of the EU. Ireland decided (presumably) to offer a discount to Apple that the EU considered later on that it could not be the case in the single market. And so ordered the Irish government to collect the missing taxes.
Apple knew the rules of the EU but took advantage of the deal (presumably) offered by the Irish government, and now will have to pay back.
Apple has indeed very smart people to minimise the payment of taxes bordering local laws as much as possible and using all kind of legal (although not ethical) loopholes. But the EU has also very smart people who analysed a lot of information and concluded this investigation. Apple just... lost.
Apple can take this to the courts as I assume they will. But remember the courts just interpret the current law, which again applies to the whole single market and so state tax aids are considered illegal.
For now Apple will be paying back

Unfortunately I imagine such money cannot be used to improve the EU's health, education and welfare system. It hurts us all when taxes are not paid as they should.