Hi S.,
Congrats on your pregnancy, and your new baby kitties!
Just to give you some background before I answer your questions, I am a LVT (licensed veterinary technician) and have worked in the vet field for many years. As far as your kitties, it isn't that uncommon for kittens to get diarrhea. A lot of times it is due to parasites, and I would definitely deworm both of them and get it under control. If that doesn't solve the diarrhea, I would bring her back to the vet to be checked out again, and maybe placed on medication to help.
My first question-have you had a stool sample checked on them? That would tell your vet what kind of parasites you might be dealing with and how to treat it. For the most part-almost all kittens/puppies get roundworms-usually from their mother, but there are other parasites that they can get as well. I would also highly recommend that you get your dewormer from your vet and not a pet store. There are different kinds of dewormers that treat different things, and some are more/less effective than others. It might be a little more expensive than the generic dewormer from the pet store, but it will be more cost effective and less headache to be treating the correct thing. Also, your vet will have products with the biggest safety margins to use in small kittens. Many of the pet store products are decent products, but can easily be toxic to baby kittens/puppies (flea products are a BIG one).
Next, as far as you being pregnant and dealing with the messes-wear gloves, and wash your hands and you should be fine. The main parasite that you should be concerned about with pregnancy is Toxoplasmosis. And, unfortunately it isn't one that is routinely picked up on fecal sample checks and it probably isn't worth the lab testing necessary to determine if your kitties might carry it. It's best just to take the precautions and not worry about it. Also, feces has to sit for 48 hours before the eggs become infective to us. So, if you scoop the litterbox daily you don't have to worry. (Although, if you can get your husband to do it, it's even better-ha!)
The other parasites that people can get from cats/dogs are roundworms and hookworms. But, same thing-get your animals dewormed, clean up poop, wash your hands and you shouldn't worry. I wouldn't tear apart your entire house cleaning, but I would definitely clean any spots where poop accidents were well.
Please don't take the advice that someone suggested that you should find other homes for the kitties. There are lots of old wives tales, but as long as you wash your hands and/or wear gloves, and keep anything that touched their feces away from your mouth (gross, I know...), the chances of you picking anything up from your kitties is very, very small.
Good Luck!! :)