The governments "just" doing this or that, are typically the tyrannical or unhinged variety you don't want to live under. If your law is written decently and you have a functioning judiciary, chances of a loopholes surviving scrutiny will be very low.

The European Commission could definitely ask governments (the European Council) to agree a new treaty or protocol that grants them veto powers on "federal security grounds", for sure. The European Parliament would likely rubber-stamp it too. Considering the current (and increasing) right-wing majorities across the continent, though, I find such scenario very unlikely.