Yes, using a new name should be a no brainer because names ARE individual part of language and not decided by the speaker.
However, the fact remains, safeguarding concerns should be investigated even if you don't like the person raising them.
Reading between the lines, rather than helping this teacher find a compromise the college went straight into 'bigot, get the ducking stool!' mode and didn't help him figure out a compromise that didn't involve social transition but protected the child's dignity. None of this has been in the child's best interests.
However, it's tricky using neutral pronouns and a new name there is a cognitive load there. But I don't think he's arguing it was accidental. I feel there are lots of gaps and potential biases / misinformation in the reporting.