Whether revised return can be accepted?

Fact of Case:
Assessment year 2012-2013
Corporate Assessee
Original Return filed in time. 139(1)

Problem:
During scrutiny- 
    AO observe MAT payable against deduction u/s 80-IC and issue notice u/s 142(1).

    80-IC income become liable to Mat as the per the amendment.

Against such notice 
    - Revised return is filed on 15/09/2014 accepting MAT payable
    - Tax has been deposited with interest
    - And Copy of 29B dated 25/08/2012 to AO

Queries: Whether Revised return can be Accepted or rejected?
             Is penalty on the ground of intentional omission can be imposed?