On a theoretical level, the Church is not able to adopt the idea that a person's subjective experience is authoritative on the advisability of choosing chemical or physical mutilation. The Church's doctrine of the human person is unambiguously hylomorphic: a female body has a female soul. The Church believes that "Nick" has a female soul, and hormones and surgery can not change it.

On the practical level, the Church has a lot to lose if it is pressured to adopt the "transgender hypothesis." Religious orders are sex-segregated, the most prestigious Catholic high schools are sex-segregated, youth ministry is often sex-segregated. In many parishes, even Bible Study is sex-segregated. (Paradoxically, many parishes have only a single restroom for mass-attenders, so this might end up being an easy one.) 

The most reasonable solution would be for "Nick" to seek pastoral support in an Episcopalian or UCC community.