As far as your case is concerned, you have reached at the stage of compromise then ready to settle all the pending cases. You should convince your wife so as to withdraw all the cases filed by her on the basis of compromise. When she decides to withdraw all these cases then you should file a petition before the supreme court under section 406 of the code of criminal procedure for transfer of all cases at any one district.
Thereafter you should prepare a compromise deed and file a divorce suit under section 13-B of the Hindu Marriage Act i.e. divorce by mutual consent. On the basis of that compromise deed, you may file a petition before the High Court under section 482 of the code of criminal procedure for quashing of a criminal case. In B. S. Joshi vs State of Haryana (2003) SCC 675; it is held by the supreme court that when parties to the marriage have reached compromise then criminal case filed by them shall be quashed.
Yogendra Yadav v. State of Jharkhand, (2014) 9 SCC 653; the High Court can quash criminal proceeding under section 482 of the code of criminal procedure in case parties have amicably settled their dispute and victim has no objection.
Divorce case shall lie however the criminal case has quashed by the high court and Divorce by mutual consent shall be granted by the court on the basis of compromise deed.