Hmm. I have lots of feedback. First would be for you to go 100% on lecturing your wife when she "slips." I promise it's not going to make her any better about going 100%. It will just make her resent you. 80/20 is the general accepted idea around here. Why isn't that good enough? I'd wager that trying to go 100% will get her closer to 80/20 or even 90/10 than trying to go 80/20 will. So relax, and back off.
Also, there is some evidence to suggest that eating no gluten/wheat whatsoever in pregnancy will raise your chances of your child having celiac disease. Rob Wolf, I believe, did a talk on this. So, while wheat is never desirable to eat anyway, I know I sure as shootin' would much rather have a kid who just doesn't eat much wheat because we don't buy it, instead of one who has a very bad reaction to it. Additionally, she will most likely crave more carbs while pregnant. The glucose in her body will go to the fetus first, which is why many women crave carbs during pregnancy. Yes, fruit and some potatoes would be better than grains, but keep in mind there is a biological reason she may be wanting more carbs. (Read "Exercising through you Pregnancy for a better explanation of this)
Paleo is definitely a great way to eat for pregnancy. How could it not be? Eating Paleo/primal means eating tons of super high nutrition foods. How important is it? Well, very important, since it contributes to the developing baby's brain function, birth weight, food preferences, etc. But don't get yourself too wound up in every little detail of your wife's diet. I'm a young, healthy, paleo eating Crossfitter who has had nothing but multiple miscarriages while my wheat-eating, channel-surfing, candy addict friends produce healthy offpsring like bunnies. So, clearly, while it is beneficial to be primal, it has its limits. Pregnancy diet is important, but it's nothing to get yourself so worked up over when your wife is already eating primal most of the time.
About the loose stools - have your wife take a good probiotic supplement. The same thing happened to me when I went primal/paleo, and my naturopath has me on a good probiotic (8 billion+ bacteria count)