It might be the case that simply putting a comfortable seat (There are many to choose from. Most any ladies touring saddle is better than any stock BMX seat.) would solve the problem.
It also might be the case that solving the seat problem would expose the problem that the BMX bike is too small for comfortable riding.
BMX bikes are made for doing tricks or for a specific kind of racing. They are not designed to be a comfortable ride. When racing or doing tricks little time is spent sitting down. BMX seats are generally the least comfortable on any bike.
It takes trial and error to find the right bike, and the right seat. She has to decide what meets her needs and feels right.
Finding a bike that fits her and has a seat appropriate for the task might help. If there is a bike shop you can visit they will let her try different bikes and find one she likes.
If there are no bike shops you might have to get creative and ask friends what bikes they have and could loan or possibly a bike rental place would let her pedal around the parking lot on different bikes.
A final thought - does she really want to go bike riding? If she does it's worth the effort to solve the problems at hand.
If she doesn't and the bike will just sit around and collect dust and spider webs no matter how comfortable it is.