I don't think God respects one marriage more or less than another solely on account of its being only a civil marriage or a church marriage, because these are all things that we stick to a marriage from outside. What will attract or repel divine favor is what is in the hearts of the couple being married. If our two athiests are firm in their committment while two people next door who got married by a priest are not, I think God will favor the atheist union (as much as he favors such things, which is a separate issue.)
An issue with church marriage is that of using the Name in vain. When a couple is married by a judge and they break their vows, they break a promise to each other and to the state. For the church wedding, they also break a vow to God. They invoked God to sanctify their marriage then pulled out on their part of the deal. We westerners are really freaky about sex, but in the old Church, it was probably this vanity about a holy service that really caused trouble.