Maybe I'm not into the whole stuff, but Apple came to Ireland and made a deal.
No matter if this was legal or not. It was a deal, so now I don't think Apple should pay anything...
The one that should pay is Ireland, as with this agreement Ireland was tricking the other EU governments.
If we want Europe, the taxation system should be the same everywhere otherwise there is no Europe. It's quite easy to get the best of Europe but not suffering the pain of it.
I don't have any opinion if being or not in Europe. Probably it is better not to stay in a centralized-Germany-driven Europe. Probably, we are in the worse of the possible different models.
Obviously Ireland can always do the same as England (Irexit) and then they would be able to have Apple for free, but then they should pay all the consequences..