You have committed a mistake by paying this amount without a proper legal channel.
If your enstraged wife has filed a FIR against you and your father, then you should have asked her to compromise only on the condition that she would support you to get the FIR quashed from the competent court i.e. High Court.
But even now when you have given her that money, you must have records to show that you arranged that money and paid the same to her. Kindly engage a good lawyer and request to file a writ in the High Court to protect your interest and prevent any further loss or ill treatment at the hands of your greedy wife and the police.
I strongly feel that time is less and you should act fast. If they arrest you or your father, then your payment would go in vain. As there was a signed MOU, then it must bear signatures of your wife and also of some witness. This would play vital role in pleading befire the High Court to quash the FIR.
All the best!