That’s crazy. What’s the problem of « a secret mariage » if both parties fear for their lives (tribes, different religion, etc).
If one made a case for exactly why the marriage was kept 'secret' and depending what exactly was meant by secret, it's not impossible IRCC would give consideration. But it will raise the question of course of how the relationship (marriage) can be real if no-one knows about it and eg. they do not live together.
The concept of no secret marriages is ancient (centuries old) and should be seen in context of traditions like reading of the Banns - the whole point of a marriage was there was a public announcement aspect (and that it could not be denied as a result). A 'common law spouse' comes from the same thing - the couple holds themselves to the public as a couple.
But iRCC are not monsters, if there's a real basis for fear of persecution etc., they will take into consideration. Note though that most such marriages eg where families disapprove will have other witnesses (friends, other relatives) present - i.e. it's not truly secret just not with all present.