Assuming genetics even work the same in Earwa, how would the Dunyain have any idea as to the minimum viable population required and details of genetic diversity related to heritage?
Further, seeing as they went to Ishual during the years of the crib, future generations would have seemed unlikely.

Anyway I think its a moot point, a quick google search reveals a study at
http://www.livescience.com/history/050525_america_settlers.html which suggests that North America may have been settled by only 70 people, not an unreasonable estimate of the original dunyain numbers.
It's situations like those that naturally create taboos and breeding patterns. As long as the population has enough mating pairs to avoid regular
inbreeding they should be fine.
Low ebb populations tend to drive evolution; starting from a small group of people like that could simply result in dominant inheritances - what we think of as racial characteristics (red hair, dark skin, whatever). Seeing as the dunyain were also actively weeding out dysfunctionals, the potential for rapid evolutionary change is only improved.
Ishual seems pretty big and we have no idea what their population levels were like as the series begins. I would imagine they would have numbered in the hundreds at least.