The difference between "Civil Union" and "Marriage" is just a confusion stemming from religious terminology. Basically, if you take away all the legal rights and tax stuff from "marriage" you end up with just the priest and the holy documents.

That the legal arrangement and the religious drivel should be inseparable is a dogmatic religious stance. It comes from the times when the church was indeed a legal authority. If the seperation of church and state is to be taken seriously, however, the state must not let itself be determined by religious considerations foremost but by its own interests which are ultimately legal. The following questions that arise and should be discussed are of a political nature and have to be answered within the appropriate context.

The "commonplace" argument is irrelevant in this regard, as the common third of every human in a society is the political unity not the religious unity - freedom of religion should include freedom from religion.