Question: "Why did God allow incest in the Bible?"
Answer: There are numerous examples of incest in the Bible. The most commonly thought-of examples are the sons/daughters of Adam and Eve (Genesis 4), Abraham marrying his half-sister Sarah (Genesis 20:12), Lot and his daughters (Genesis 19), Moses’ father Amram who married his aunt Jochebed (Exodus 6:20), and David’s son Amnon with his half-sister Tamar (2 Samuel 13). It is important to note, however, that in two of the above instances (Tamar and Lot), one of the parties involved was an unwilling participant in the incest—better described as rape in those cases.
It is important to distinguish between incestuous relationships prior to God commanding against them (Leviticus 18:6–18) and incest that occurred after God’s commands had been revealed. Until God commanded against it, it was not incest. It was just marrying a close relative. It is undeniable that God allowed “incest” in the early centuries of humanity. Since Adam and Eve were the only two human beings on earth, their sons and daughters had no choice but to marry and reproduce with their siblings and close relatives. The second generation had to marry their cousins, just as after the flood the grandchildren of Noah had to intermarry amongst their cousins. One reason that incest is so strongly discouraged in the world today is the understanding that reproduction between closely related individuals has a much higher risk of causing genetic abnormalities. In the early days of humanity, though, this was not a risk due to the fact that the human genetic code was relatively free of defects.
Another consideration is that incest today almost always involves a pre-pubescent or powerless victim, and the perpetrator is abusing his or her authority with the goal of unilateral sexual pleasure. By that standard, the “incest” of the Bible has nothing whatsoever in common with modern-day incest. There was no power difference between Cain and his wife, for example; the goal of Abraham and Sarah’s marriage was to create a family. Intermarriage among close family members was a necessity in the generations immediately following Adam and Noah and was not a sinful perversion of sex.
It seems that, by the time of Moses, the human genetic code had become polluted enough that close intermarriage was no longer safe. So, God commanded against sexual relations with siblings, half-siblings, parents, and aunts/uncles (Genesis 2:24 seems to indicate that marriage and sexual relations between parents and children were never allowed by God). It was not until many centuries later that humanity discovered the genetic reason that incest is unsafe and unwise. Genetics was not an issue in the early centuries of humanity, and the marriages that occurred between Adam and Eve’s children, Abraham and Sarah, and Amram and Jochebed were not selfish pursuits of sexual gratification or abuses of authority; accordingly, those relationships should not be viewed as incestuous. The key is that sexual relations between close relatives were viewed differently pre-Law and post-Law. It did not become “incest” until God commanded against it.