The suit addresses this pretty well on pages 25-26, but basically the problem is that
affirming a social transition is not a neutral act.
From the pdf: "... some evidence shows that social transition “locks” the
child into discomfort with his or her biological sex (that is, entrenches rather than cures gender dysphoria), and greatly increases the likelihood that the child will continue on to puberty blockers, cross-sex hormones, or both."
So even if the school wasn't explicitly going against the student's therapist, you can still strongly argue that this counts as a psychological intervention that they have no business doing.