Welcome to the forums!
Is Mary Jane currently housed in the same cage as her parents?
If so, then to avoid potential future problems, it would be best if you placed her in a separate cage, so that your breeding pair is fully focused in raising this current clutch.
If all eggs hatch, do you plan on keeping these 7 chicks or will you have some good homes lined up for some of them?
If you are planning on keeping them, then strict measures must be taken in order to ensure there are no matings between siblings and to prevent inbreeding between them or between a parent and one of the offspring.
This can be achieved by separating and housing your budgies by gender (males in one cage, females in another).
To answer your question, the mother budgie will not suffer from being separated when the time is right to do so, she will quickly move on and resume to her normal routine. This is a common practice not only to prevent another clutch from happening, but also to avoid chick aggression once they reach weaning age. By this time, the father is perfectly able to finish raising the chicks with your help and support and since you are expecting a much larger clutch, you may really need to have a more active role in helping to raise these chicks.
When you separate the mother budgie, be sure to not give her anything that she can use as nest. Since you have Mary Jane and if they get along well, mother and daughter can be housed together for the remainder of the time till the chicks are weaned and independent. The chicks can be moved when they are perfectly confident in their skills, are fully weaned and no longer use the nest for comfort. By the time they are 7 - 8 weeks old, you can move them to their own cage.
It would also be a good idea to take any mirrors out of the cage and replace them with other types of toys. More often than not, mirrors and mirrored toys can cause harm especially when budgies develop an unhealthy attachment to them. And in your specific case by removing the mirrors, the drive to mate can also decrease (especially if the male considers the "other budgies" on the mirror as competition or possible suitors to his mate).
Before placing the mother budgie back with her mate, the nest box should be removed from the cage and no nesting sites should be available to them.
Also by following the recommendations on the link Julie has given on her post, you should be able to successfully keep your pair from breeding.
For additional info and to be better prepared, you can check the sticky threads here at the Breeding section.
These two links may be of use in your breeding journey:
Best of luck with everything and if you need further help, we will be here to assist you.