There is no intrinsic reason why egg yolks are unsafe. The only problem is that uncooked food can be contaminated with some pathogen that would require antibiotics that would be harmful to the fetus. Salmonella is the main worry with eggs.
There are a few reasons why the risk is even less than you might think. From an egg-producers' PR organization:
Q: Are Salmonella bacteria most likely to be found in the egg’s white or yolk?
A: Bacteria, if they are present at all, are most likely to be in the white and will be unable to grow, mostly due to lack of nutrients. As the egg ages, however, the white thins and the yolk membrane weakens. This makes it possible for bacteria to reach the nutrient-dense yolk where they can grow over time if the egg is kept at warm temperatures. But, in a clean, uncracked, fresh shell egg, internal contamination occurs only rarely.
Also, if you can get eggs from a small organic / free-range farmer, instead of in the supermarket from vast arrays of caged hens, first of all, there's less likely to be salmonella around. Secondly, if you can be sure the eggs are very fresh (picked up same day, immediately refrigerated), it's less likely that any salmonella present would have had time to grow. From the first link, the rate of salmonella in eggs is about 1/20,000, and with using smaller farms with fresher eggs one should be able to cut that to 1/200,000 or less.
Of course, the woman/couple in question need to decide what level of risk they're willing to tolerate, but with a little care, one is almost certainly safe eating yolks. Eggs are a great source of nutrition, and the yolks are rich in many vitamins (including folate which is probably being supplemented anyway), so if buying free-range eggs from farmers that can house their birds at low density is an option, and if having runny yolks will increase the woman's egg intake, I'd speculate that on average it's probably better to eat runny yolks than to forego eggs for fear of salmonella. Eating just as many eggs but cooking them more thoroughly would be better yet.