The problem is not the 3-month grace period. The problem is that you traveled on an Indian passport while you also possessed a Canadian passport. That is illegal according to that 3-month grace period rule. There is a possibility of getting into a lot of trouble while exiting India!
The reason they give you that 3-month grace period, after obtaining another country's citizenship is because you may not be able to obtain that other country's passport in a timely manner. So they allow you to use the Indian passport.
That is why (as others have suggested), the easiest and best thing for you to do would be to EXIT INDIA TO A PLACE LIKE NEPAL ON YOUR INDIAN PASSPORT (don't say anything about your Canadian passport). Then book a ticket from Nepal to Canada and exit Nepal on your Canadian passport (I don't think Nepal would care about that, because you never had anything to do with that country).
You will still have to deal with the consequences when applying for OCI and surrendering your Indian passport, but at least you would be able to return to Canada without any hassles.
NOTE: while notifying the authorities and applying for an "exit permit" is an option, this is highly bureaucratic India we're talking about. You don't know what kind of problems that will lead to and how kindly they will look upon breaking the law!
That's why, in my opinion, I think the above suggestion is much simpler! You are not breaking any law by traveling to a "3rd country"!