There is a difference from a Rabbinic Marriage and a marriage granted in law. Just like the churches in America can deny marriages to couples that are gay, or for what ever reason. While the State can grant marriages without the prejudices or reasons of a marriage of religion.

Also the law of having only Jews marry Jews is a law of survival, at the rate that our people are marrying into other faiths and then raising their children of that faith is slowly eroding our people. We do not have ten's of millions of Jew's, we can not afford to allow us to grow smaller than we already are.