Hope she has received Maternity Benefit from the employer. If this assumption is right, then employer is also right.
If the terms of employment says that you need to serve three months notice to company, you are required to adhere to it. Or if you want to be relieved earlier, then there is NOTHING WRONG in adjusting the amount payable for the balance notice period, against the dues payable to you.
How can you expect the employer not to deduct the notice period pay? I am asking a question. If the same employer communicates you (or your wife for that matter) that you are not required in their services any longer (or from a particular date) when you come to office for signing the muster, how would you react? Will you not expect some notice period required to apply for new jobs, collect your offer / appoitment letter, so that the exit process would be smoother?
If you agree to this point, then employer also has his right to expect you to serve notice period, for him to locate a potential candidate to be put on the job, train him and take over charge from the outgoing candidate.
I always believe when you do good things (irrespective of others doing good to you or no), you will receive good deeds. It is like a "rubber ball" thrown on a wall. (you play this and see yourself). When you throw a rubber ball on the wall, the speed or pressure with which you throw, with the same speed, it comes back to you. (I have played myself and learnt a message from this).
It is upto you to decide to adhere to the company's rules or kick the employer and vanish without any information.
Balaji