You have to following steps:
1) For taking permission from Collector, you must make the application in writing, after they give a written reply rejecting the permission and advises to take NOC from Church authorities, you may apply for NOC in writing to the church authorities, get their reply also in writing;
2) After finding no respite despite your above efforts, issue a legal notice to church authorities demanding NOC and implead collector as a party to the legal notice;
3) If you get a favorable reply to your notice, you may go ahead with your proposed task with the property or else approach court seeking declaration and mandatory against the authorities to not interfere with your possession and construction of the proposed structure in your property.
You may follow the above steps with the help of a local advocate.