From a practical point of view, the risks are small enough to not warrant society interfering with their lives, from what I can tell.

All the studies I've seen put the number of fatal recessive genes in the average person at around 4.  These do not result in societal cost due to inbreeding, because when expressed they generally result in an early pregnancy miscarriage.  

If you accept the data showing a 2 percent chance of a major birth defect for cousins, the rate for a mother / son or father /daughter pairing can then be calculated at 16 percent.  This also requires that the average number of such birth defect genes carried (though not expressed) by the average person be 1.28.  This number doesn't seem so very far off but from it we can calculate that the chance of such a genetic defect being expressed in someone who is born from a very large number of consecutive brother / sister pairings should be 1 - exp (-.64) =  48%, which seems rather low compared with anecdotal evidence such as Charles II of Spain.

Of course, recessive genes which leave the person with them expressed worse off but still in the "normal" range would not be caught at all by this method, and we have no idea at all how many of them there are from this data, or how badly effected by them the average child of cousins would be.

Of course, the child of anyone with someone with someone unrelated has no inbreeding risk, even if one parent is Charles II of Spain.  In a situation like Thoroughbreds or AKC puppies, the problem is that that there are no animals to breed to which aren't closely related (except the mutts).  The inbreeding problem is with the whole gene pool.

A related situation would be cheetahs or American Indians, where there was a severe inbreeding a very long time ago, and any resulting genetic diseases have been long ago evolved out of the population, but genetic diversity remains low.  This leaves populations vulnerable to disease, not because their immune systems are bad, but because all members are vulnerable to the same diseases.

In regards to polygamy: incest has the opposite genetic effect than polygamy. Polygamy means more genetic diversity through the different mothers. Incest means less genetic diversity.

So then they balance each other out?

All anyone has to do is think about inbreeding that we already know about: purebred dogs and thoroughbred horses. Both purebred dogs and thoroughbred horses are prone to more diseases.

And yet they're probably the least likely species on the planet to go extinct any time soon. The inbreeding, while an individual negative, has a larger purpose that keeps the species peculiarly protected. Think corn and apples.

In terms of threats to humanity's genetic perpetuation there are tons of massively larger threats. Do I morally condone incest or polygamy? Honestly, I don't care to give them that much thought. I have no personal interest in them and I'm not going to waste my time condemning those who might go down that road. There numbers are so small as to be a tiny diversion in the march of human genetics. I don't think either matters, though. In the long run, Saletan is right.

It is easy to buy small plaster models of what you think life is like.

From your second link, I enjoyed this quote of G.K. Chesterton:

In the matter of reforming things, as distinct from deforming them, there is one plain and simple principle; a principle which will probably be called a paradox. There exists in such a case a certain institution or law; let us say, for the sake of simplicity, a fence or gate erected across a road. The more modern type of reformer goes gaily up to it and says, "I don't see the use of this; let us clear it away." To which the more intelligent type of reformer will do well to answer: "If you don't see the use of it, I certainly won't let you clear it away. Go away and think. Then, when you can come back and tell me that you do see the use of it, I may allow you to destroy it."

This paradox rests on the most elementary common sense. The gate or fence did not grow there. It was not set up by somnambulists who built it in their sleep. It is highly improbable that it was put there by escaped lunatics who were for some reason loose in the street. Some person had some reason for thinking it would be a good thing for somebody. And until we know what the reason was, we really cannot judge whether the reason was reasonable. It is extremely probable that we have overlooked some whole aspect of the question, if something set up by human beings like ourselves seems to be entirely meaningless and mysterious. There are reformers who get over this difficulty by assuming that all their fathers were fools; but if that be so, we can only say that folly appears to be a hereditary disease. But the truth is that nobody has any business to destroy a social institution until he has really seen it as an historical institution. If he knows how it arose, and what purposes it was supposed to serve, he may really be able to say that they were bad purposes, that they have since become bad purposes, or that they are purposes which are no longer served. But if he simply stares at the thing as a senseless monstrosity that has somehow sprung up in his path, it is he and not the traditionalist who is suffering from an illusion.