If any woman has a husband who is an unbeliever, and he consents to live with her, she should not divorce him. For the unbelieving husband is made holy because of his wife, and the unbelieving wife is made holy because of her husband. Otherwise your children would be unclean, but as it is, they are holy. (1 Corinthians 7:13-14 ESV)
How would this verse play into things though?
And isn't sex what makes marriage in the eyes of God, not the ceremony?
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Then the man said, "This at last is bone of my bones and flesh of my flesh; she shall be called Woman, because she was taken out of Man." Therefore a man shall leave his father and his mother and hold fast to his wife, and they shall become one flesh. (Genesis 2:23-24 ESV)
Or do you not know that he who is joined to a prostitute becomes one body with her? For, as it is written, "The two will become one flesh." (1 Corinthians 6:16 ESV)
All things considered, their marriage has already been sanctioned in the eyes of God. Doing the ceremony would (1) legalize their marriage and (2) bring the church into covenant with them to promote the health of their marriage and in raising the child in hopes that he/she will come to faith.