Something to Consider...
Was Lucius Hunt actually Edward Walker's son?
The Sigourney Weaver (Alice Hunt) character was a single mother. Even in the old photo of the founders of the village, we see Alice Hunt alone with baby, while the others are paired off. In the course of the film we see hints at an unspoken, romantic relationship between Walker and Alice. Alice Hunt tells Lucius that his father died in "the towns", but she was single before the experiment began.
So why would Walker want to of his offspring to marry and possibly have inbred children? He had developed a god complex as a leader, and I believe he wanted his bloodline to rule over future generations.
We've seen similar behavior in rulers throughout history. In fact, we've seen similar inbreeding in FLDS (Mormon) compounds, and throughout the history of Mormonism, where a few strong men impregnate many women.
I'm not saying this is all necessarily true, but it something to think about.