Of late there have been some similar queries about female employees giving notice of termination during the period of maternity leave. I have told them that there shouldn't any problem if they didn't mind. After all, since the employee has not intention of carry on working after confinement, so be it.
But some employers like you may think differently. Some employers want the employees to come back after confinement to serve the required period of notice and work through because they don't want the employees to use maternity leave to offset the notice period. In your case, since 3 months notice have been given, you may accept it but the 60 days maternity allowance will not be paid as it is going to be used as indemnity in lieu of notice and she will come back to work until 1 May. Honestly, I had not made any ruling on such a case during the years of service and if I had, I would have ruled that maternity allowance was not to be paid as it would be used as indemnity in lieu of notice.
For this case, I think you better pique the brain of the Labour Department as to how to go about your case. I strongly recommend that you consult them. Feedback from you will be appreciated.