The evolution of inbreeding avoidance is complicated

[...][A]n attempt to mount a purely eugenic argument would be confused because the maladaptive genes expressed when inbreeding is common are not removed from the population by preventing inbreeding. Indeed, inbreeding is the best way of getting rid of those genes in the long run.

- Patrick Bateson, Inbreeding, Incest, and the Incest Taboo

Inbreeding avoidance evolved in part because it helped individuals and their children and grandchildren, on average, not because it made the population as a whole genetically healthier; the genes for inbreeding avoidance propagated more, on average, over time, than their competitors.  Evolution, like life, is more complicated than our taboos.