1. From your brief the procedure followed by the Church is valid legal procedure and the issued Marriage Certificate has legal validity and recognition of being Certificate of Registration of Christian Marriage in India. They will not give you copies as you are asking other than Marriage certificate that they gave to you. Rest two copies are duly procedure followed by the concerned Church so it is useless to ask such copies.
2. To me it looks like you are worried of future usage of Marriage Certificate say as illustration for the purpose of traveling visa or immigration for any foreign country, then the Marriage Certificate would be required to be Apostillised first, so carry out the process of Apostillisation of this Marriage Certificate first then use it for any such visa or immigration purposes.
3. In Apostillisation all documents should be first authenticated by the designated agencies in the State from where the document has been issued. Like in case of personal documents like birth, death, affidavits, power of attorneys, marriage etc, Home Department/General Administration Department are the designated authorities. You can log on to State’s official website and there they normally give all such information.
4. Further, in case of educational documents like degree, diplomas, matriculation and secondary level certificates, State Governments have now opened Regional Authentication Centers (called as RAC’s) at various States from where the document should first be attested.
5. Documents attested by these authorities then need to be presented to MEA for issue of Apostil’s at Ministry of External Affairs at CPV Division, Patiala House New Delhi. Once the Apostils stickers of Rs 70/- (check latest Fees structure if has changed) is affixed each on all these documents you can use them for VISA / Immigration purposes if asked by concerned Embassy.
Hence, do not worry the Marriage Certificate is a valid one for all legal purposes.