It's not what you say but the way that you say it
Apple would collaborate with the Irish government if it launched an appeal against the ruling
I don't actually think that the ruling can be appealed, it has to be challenged in the court. And, as Apple is the benefactor of the subsidy, it's up to Apple to challenge it. But nice of Mr Cook to suggest that Ireland has somehow been punished by the ruling and that Apple is on their side.
As for the prospect of a challenge the ECJ has a history of confirming the Commission's rulings, especially when it comes to upholding the principles of the single market, of which unfair state aid is an obvious example. And companies invariably play along as the alternative could be reduced access to the market, or being forced to repatriate the earnings so that they can be taxed in the US.