She can also have herself and the kitten tested for toxiplasmosis, which is the problem with changing the litterbox when pregnant. Many adults have an acquired immunity already to it. Also, if the kitten has always been indoor only, the risk is minimal. Toxiplasmosis is a bacteria that is generally transmitted when cats eat mice and other furries, or come in contact with other cats' excrement or contaminated soil.
The other thing is that it takes 24 hours, give or take, for the soil/litter to become contaminated from the feces of an affected cat, so scooping frequently will help minimize the risk. And as 3 Kitties said, wearing rubber gloves and even a surgical mask when doing litter duty, and washing up immediately afterward is generally all the protection she needs. Be sure to discard all used kitty litter immediately, so she doesn't have to handle it twice.
Don't let her Dr. scare her with misinformation! Many doctors have good intentions but give out misinformation on the dangers of cats and pregnancies.
(I just happened to read about this last night! What good timing.