So the priest is fine with gay relationships, but a person possibly being trans gives them pause?
Just like IRL! Although given the recent news about the church and trans people, maybe that'll change.
Also, his intent was less about him realizing Angel is trans and more "there's 2 distinct voices in that mind? Is this young girl possessed by some sort of demon? We must investigate this further." Although, perhaps I should have been more explicit about that... oh well, maybe for a B-sides 4koma...