Ah yes, because laws are totally independent of morals. I'm clearly being facetious. Laws are the manifestation of morals, either collective or of highly influential individuals.
But, to your point, laws are the non-arbitrary manifestation of those morals. Indeed there should be no unwritten standard as well. In this case, there wasn't: the Irish laws did not comply with EU law, and EU law take precedence in this matter. Apple should have known that was a possibility, and probably did know but hoped (and lobbied) for the best.
Morals are very relevant when deciding what's right and what's wrong. In this particular case, I fully support the European Commission. Note that there are laws against setting up artificial corporate structures with the sole purpose of circumventing taxes, and that's exactly what Apple did (with the help of the Irish tax bureau). The only problematic thing here is that Apple is being made an example of. There are many other companies that are doing the same. But it makes sense to handle the largest cases first.
I wish I could, unfortunately I have no power or money, while multinationals have armies of lobbyists and bags of money a la Scrooge McDuck to help write the laws to suit them.
Actually, it's not obvious at all. The parent is suggesting that the EU should not adhere tax law as written and should instead attempt to impose it's morality.
They do pay taxes. You are advocating that they should pay taxes that they don't owe because an EU bureaucrat wants to increase the power of the EU against the sovereignty of the individual states, in this case Ireland.
Tax law is a system of rules. There should be no second arbitrary standard people (and companies) should be expected to follow.