Earlier quoted context omitted.
What are you arguing exactly? This isn't punishment or fine, this is paying what they should have all along.
The target of the case is wrong, it should be Ireland, not Apple. Many companies have unique (to them) tax benefits across the entire EU, some hidden under things like “electricity subsidies”. If the company pay what the country mandates, then the rest should be between the country and the EU, not the EU and the company.
Law often does that to perpetrators. Ireland tried to save the shady deal by refusing the money it should have received (corruption in plain sight, with these sums its not unexpected it goes to highest places plus something about saving nation's public face), so this is how they got about it.
Not sure its 100% best process but overall a very good move and precedent for future.