We western democracies try to foster free trade, because we know it is a Good Thing (tm). That means removing obstacles such as import duties, but also removing other practices such as non-tariff barriers to trade and unfair state aid to companies. Those are agreed upon under the auspices of trade agreements and transnational bodies such the WTO. When a country is not playing fairly, eg. engages in dumping, these organizations intervene because it is their job to do so.
The job of the European Union is to create a common internal market with a level playing field. The level of integration is higher than other treaties, but the principle is the same. Ireland agreed to specific terms when it entered the union and got the benefits of participating in the market. If the findings of the commission are based on fact and Ireland has broken the rules, then corrective action has to be taken.
Crying about lost sovereignty is disingenuous and besides the point.