I dont know how EC can justify (in court) violating non-retroactivity traditions/laws.
That's why the Commission rarely acts in such a direct manner - they know they are talking to very powerful interests. But again, in most cases, when such procedures are invoked, national governments are eventually found in violation. Nobody enjoys victimizing a member state, they only do it when infractions are so egregious that they cannot be ignored.
> violating non-retroactivity traditions/laws.
If you don't pay taxes in 2012 and the state sues you in 2014, as long as the statute of limitations allows it, there is no retroactivity. The Commission only started to actively investigate these arrangements recently, but the relevant laws have been on the books (or rather in the treaties) for a very long time. Just because a policeman doesn't arrest you for beating your neighbour doesn't mean you're not breaking the law.