What happens when a couple (first cousins: the woman got pregnant and then married) studies the Bible and wants to repent. Are they to separate or stay married?

That would depend in part on which nation they lived in, as marriage to first cousins is no longer prohibited in many countries, despite the greater risk of birth defects among the progeny of such unions. If you are referring to the United States, I do not think any law officer would force a separation. Biblically speaking, there is no clear passage forbidding it (you will scan the New Testament in vain!). And this is a legitimate marriage: the man is not a bigamist; the partners are of opposite genders; they have legally become married, not just moved in with each other and called it "matrimony." In my opinion, they should stay together. (Not to mention their mutual obligation to their child.)

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