From your post, it seems to me (correct me if I am wrong):
1. She has resigned while on maternity leave and after availing (as advance) all maternity benefits from the company.
2. She may not be averse to reimbursing the company for the short notice period.
3. She is not okay with paying back any of the maternity benefits accrued to her even though she has resigned midway or at the beginning of the maternity period and is not in the mood to settle on a pro rata basis.
4. Management wants to recover the part not accruing to her but paid in advance.
5. I assume here the maternity period has only just begun (pre-delivery).
My Suggestion:
1. Send her a notice asking for payback for the short notice period.
2. If she has availed benefits in advance, ask her to reimburse the company (in the same notice) for the portion that may not be accruing to her due to her resignation.
3. If she pays back money in lieu of availing benefits which are not yet due but which she has availed in advance - very good.
4. If not, do not persist with notices and cases, etc., as there are a lot of advantages under the law for a woman under these circumstances (you cannot force the issue in your favor).
5. Consider the woman as one not worth her salt.
6. As for work stopping due to this lady being on maternity leave, surely as suggested by others, you must have thought over this exigency.
Hope this helps.