The thing is, the marriage clerk himself destroyed the document. He is a religious person and did not agree with the marriage after seeing the my birth certificate. So, there is nothing registered anywhere. I can re-marry her to get the docs but we are so afraid of them finding out and forcing her to into another marriage or maybe physical abuse.
Well I'll be interested to hear the opinions of others on this case.
But given the situation I'd go with the conjugal app and explain this all. I'd make the argument that the marriage did not legally happen if papers were destroyed by the clerk. The rest of the evidence is in support that there was a desire to be married by you two - and actual actions - but you were prevented from doing so.
While i can't guarantee, I think this is in some respects the type of situation for which the conjugal app type was established. And I should hope iRCC staff analyzing the situation would be sympathetic.
You're not the first person to have had parents and family who do not approve, on religious or other grounds. Just make sure to explain everything, and document what you can.
(While you can and should of course provide the background about the gender aspect, I don't think you need to spend a lot of time on that. Just be factual. The core of the story is parents and society [in the person of the clerk] disapprove.)