Yeah, the main reason for no catbox changes is the bacteria and ammonia that can be inhaled and cause harm to the fetus. As long as she doesn't strain herself with the water changes... and of course she should probably steer clear of the handling of any chemicals as some can be absorbed into the skin.
But yeah... doctor knows best. But make sure the doctor understands how involving the aquarium process is because not all doctors know. (aka, have a list of chemicals she would use to maintain or clean the tank, inform him of the water changes and the need to haul water, and also of the cleaning of filters and possible bacteria and ammonia build-up in them)
Afterall, anyone needs all the pieces to make a complete puzzle, right? With that information, s/he'd be able to give you the best guidelines on how she can maintain her fish AND be a healthy mom for her little bambino!!
Congratulations to you both and good luck.... OH!! And post the doctor's opinions? Other women/fish-lovers might want the FYI for when they are hauling water at their third trimester!!! ^___^