The provably variable nature of sex chromosomes, gonads, genitalia, and secondary sexual characteristics clearly indicates that gender is neither fixed nor binary. This is a biological fact backed up by vast amounts of scientific research. Transgender people always have and always will exist; schools can either protect their trans students from those who would deny their very existences, or they can be a force for the destruction of trans lives. I mean that entirely literally, given that trans students--particularly trans students of color--have verifiably higher rates of self harm and suicide than any other group. Transphobia, whether it is overt or the passive refusal to acknowledge the trans individual, has dire consequences for its victims. Please consider that trans children will not go away, but with progress in normalizing the protection of their physical and emotional well-being, transphobia very well could.
The feelings of those who have chosen to use religion to excuse their own discomfort with the fluidity of gender simply cannot take priority over the health of trans students. Gender affirmation doesn't just feel good--it saves lives.