The more honest question would be this one- why was it permissible for Cain (and Seth, and many more for that matter) to marry his sister? It is a more honest answer because we know there could be no other choice. We know also that God established, over time, differing standards of marital consanguinity. As late as Abraham we have a man married to his half sister. Why would God seem to adjust His law?
And that question is one He has not given us an answer for. We can, however, speculate a bit, so long as we remember that is what we are doing. Could it be that the law changed because the danger changed? We need to remember that our most ancient fathers did not live in exactly the same world we live in. These men lived for hundreds and hundreds of years. They may have lived in a time where there was no rain. They lived in a time when their bodies were just a few generations removed from the perfect, unfallen bodies of Adam and Eve. Is it just possible that those realities meant the dangers that come from a too close interbreeding were significantly less than they are in our own day?
It is important that we grasp both the continuity and discontinuity between that world and our own. Adam was a man, Eve and woman. Just like, after the fall, you and me. They were neither spiritual monsters nor spiritual heroes. But there is discontinuity as well. They didn’t have the accumulated damage that comes from sin, whether you tend to side more with nurture or with nature. The world was very much like our own, but it also had not suffered through the cumulative effects of centuries of curses on the ground, nor centuries of the destructive habits of sinful men.
We must grasp as well the distinction and the overlap between natural law and positive law. Natural law describes God’s law in terms of natural goals. Positive law is a specific application. God, for instance, in the Old Testament required his people to put up fences on their roofs. Is that law still with us? Yes and no. In terms of the goal, protecting people from danger (as roofs in those days were used as living spaces), the law still stands. The application of it, or the positive law version of it would be a requirement that we put a fence around an in-ground pool, lest someone could come upon it unaware, fall in it and drown.
The laws of consanguinity (how close a relation one is permitted to marry) are positive law reflecting natural law. The natural goal is to not pass along genetic flaws shared by close relatives. How far distance needs to be would impact the positive law. Cain and Seth didn’t sin in marrying their sisters, nor Abraham in marrying his half-sister, not because God was more easy-going that long ago, but because the danger was so much less that it would be in our day.
All of which ought to remind us that God’s law is given for our good, for our blessing. Which is why we should not just obey it, but give thanks for it.