This is such a nonsensical argument, it's entirely akin to arguing that once a burglar has committed a burglary it's too late to arrest them and seize the goods back because to do so would be a violation of ex post facto.
The reality is that many crimes are dealt with after they happen, some crimes require many years to investigate in deal with in part because of their complexity, and in part because of lack of availability of information or resources required.
However much Apple fanboys may wish to argue this is a retroactive change it's simply not, it was illegal as far back as 1979 for Ireland to offer preferential rates to certain companies that other companies had no access to - that's before Apple engaged in this form of tax evasion and so it's lawyers and accountants should've full well advised it that it was breaking the law, if they didn't then that's their problems, no one elses.
This is really the fundamental point - that long running mantra in defence of tax evaders of "They're legally avoiding tax!" has now been proven false, that doesn't mean you get to declare their tax evasion as mere avoidance, on the contrary, the reality is that what you previously declared mere legal avoidance has now been deemed illegal evasion, and that's the problem here - these companies have been engaging in illegal tax evasion with the assistance of the Irish state and now they've finally been caught and sentenced.
For a long time because no action was taken against these companies you could indeed simply shout "It's just avoidance, they're doing nothing wrong!". That's simply no longer true, we now know that it was evasion after all, that they were in fact doing wrong, and that they're being rightly punished for it. This doesn't just apply to this particular ruling but to the fines enforced against Google, Fiat, and all the others - the reality is that these corporations are tax evaders, no matter how hard they may have tried to push the PR view that they're merely engaging in avoidance, they weren't, their actions are criminal evasion and people like you will just have to accept now that you were wrong all along about it all merely being legal avoidance. You don't get to declare it any other way, because you're not the law, and the law isn't on your side, those you were defending broke it and have been busted. Get over it - you don't even owe them anything.