1. It seems from your subsequent briefs the chain of event that happened till elders in family may get the wind of them are that the couple signed the Civil Register in the Church after their marriage. Here it seems the marriage is performed under S. 5 (1) and 3 months ago it was registered under S. 30 of the Indian Christian Marriage Act – Right!
2. Hence under normal circumstances I will still reiterorated that there is therefore no need to have a separate “Court Marriage” for legal purposes. But your situation is one that of pleasing elders as well as present marriage life simultaneously so there you go (read on);
2a. However the situation emerging form your next brief clarified further on your primary que. and in that case after the Church Wedding the solution for the couple is that they can take the Church Marriage Certificate and go together and get their marriage Re-registered under S. 15 of the Special Marriage Act. From the date of this Re-registration, their marriage will be converted into a marriage under the Special Marriage Act. The process of Re-registration involves giving one month's notice, taking the Church Marriage Certificate, witnesses etc. (as though you are getting married under the Special Marriage Act) and going through a ceremony before the Registrar.
2b. But do note this is a one-way process from another Marriage Act to the Special Marriage Act. The reverse cannot be done.
2c. The so called "Court" Marriages that some couples enter into under the Special Marriage Act before the Church Marriages have led to some problems, when after the civil marriage one party either vanishes or refuses to go through the Church Marriage and holds the other party to ransom, as this other party is bound by a civilly legal marriage that is not recognised by the Church. I hope this is not the case in hand J
On the contrary yours is a very interesting brief I got privilege to reply with above correct provisions of Law / procedures wise.