Tim Cook is dumb or just playing dumb. Contrary to what he claims there's nothing new about the ruling, and the EU has already a tax control code in place, which Ireland - in cooperation with Apple, Google, and co - deliberately ignored. The ruling adds nothing new there, it merely confirms that the attempt to get around the code - that has been existing for multiple decades now - was illegal and futile.
Cook is also wrong that Apple and Ireland would have the same interests. They do not. Ireland's interest are collecting all the back taxes from Apple - and the latter of course wants to avoid having to pay that.
Apple can try to appeal the issue, but really, the only thing they can achieve is that they'll have to pay even more interests on back taxes. The rules are and were always clear. Apple definitely tried to break the EU tax code (in cooperation with Ireland), and now they got caught and will have to pay for it.