The corporation tax rate in Ireland is 12.5%, and the rate applied to Apple was (eventually) 0.005%: it's the delta between Irish own tax rate and the one applied to Apple that is deemed illegal according to this EU ruling.
If Ireland want a 0% tax rate for all corporations, as far as I know they are allowed to do it. They just cannot afford it.
That's the EU's interpretation of the figures, but that's assuming Ireland should have taxed all revenue across all of Europe. The Irish tax system doesn't work that way though and the Irish government is stating flat out that there were no special deals: the apparently "low" rate is because the EU isn't calculating taxable income the same way Ireland does.
If Ireland want a 0% tax rate for all corporations, as far as I know they are allowed to do it. They just cannot afford it.