Mcs act, 1960

Directions issued by Deputy Registrar u/s 79(2)(a) and 79(2)(b) were not complied by the Society. Thereafter Order was passed u/s 80(2) and action was initiated by Collectors Office. Police constables visited the Society premises to enforce compliance. There after Registrar issued show cause notice u/s 79(3) and Society refused to comply and file was closed for Order. After the file was closed for Order, the Society finally complied. However, the Registrar passed Order u/s 79(3), since the offences were already committed and proven. Society filed appeal at Div. Joint Register, claiming that compliance has been done, and Order u/s 79(3) should be quashed and set aside. My question: Does the Divisional Joint Registrar have the power to grant pardon for offences which are already committed, admitted and proven. Just because the Society complied, does it mean that they are not liable to punishment ? Is there any law that states that : any offence once committed, admitted and proven is liable to be punished? Does it mean that the Society can harass and torture the Members for 3 years and at the very end, after the file is closed for Order, they comply ... and then they are pardoned. Is there any provision for the Div. Joint Registrar to grant pardon?