"or give up its sovereign right to set its own tax policy". No, the big bad wolf, the EU, does not take away the sovereign rights to set tax policies. But in case you have not realized it, each time some company is playing the game, all of you will write "it's the law that is at fault", and should be mended, until somebody, like the big bad wolf, suggest something could be done about it.
In this case it's fairly obvious that the Irish government has to oppose the ruling first, even if they want the money, or not, later. Apart from that it was about an illegal state aid, again because the EU does not interfere in the tax policy in its member states, perhaps they should, perhaps it will be more possible without the UK.
Most people are fairly fed up with all the gaming of the system. Perhaps both the UK and the US governments should have got it, a bit earlier. I am totally confident that there is more intelligence within the EU, although the problems are large.