I understand that the issue here is the nature of the deal with a specific company, but the EU does not want member states to have too much leeway to cut taxes in any case. They have set minima for corporation tax and VAT, for instance.
Ultimately this is a question of competitive advantage and of ways for small, peripheric countries to survive and prosper. If everything was the same everywhere in the EU, then why would companies pick Ireland?
The US have "domestic tax-heavens" and the country is not falling apart... The EU isn't at risk, either, including because of the huge VAT levels compared to corporation tax.
Effectively, I think this boils down to powerful EU states who want to have high taxes and don't want others to undercut them.
It's odd that the view here, at least among Europeans, seems to be that the higher the taxes the better when the issue is obviously much more complex.