Conservatives do not take the introspective reports of transgendered people seriously, but there are good scientific reasons for supposing that subjective experience of gender is legitimate, even when it contradicts apparent biological sex.
“Call Me Caitlyn” By J. Peter Nixon
The question as I see it is whether a person with a gender identity that is at variance with their chromosomal/physical gender necessarily violates the moral law if they choose to live according to their gender identity and (although this is a separate question) ultimately undergo gender reassignment surgery.
Perhaps the Church will come to recognize that a decision to pursue gender reassignment surgery need not be motivated by an understanding of gender that is incompatible with our theological anthropology.
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The first reason would be a reaction against what is wrongly seen as monosexual soul-stereotyping. A wholly male soul, whatever maleness means, or a wholly female soul, sounds unreal and oversimplified. But that is not what sexual souls implies. Rather, in every soul there is—to use Jungian terms—anima and animus, femaleness and maleness; just as in the body, one predominates but the other is also present. If the dominant sex of soul is not the same as that of the body, we have a sexual misfit, a candidate for a sex change operation of body or of soul, earthly or Heavenly. Perhaps Heaven supplies such changes just as it supplies all other needed forms of healing. In any case, the resurrection body perfectly expresses its soul, and since souls are innately sexual, that body will perfectly express its soul’s true sexual identity.
Peter Kreeft, Catholic philosopher and apologist