Maybe, but she does harm. Many people believe many things for many reasons. There are people who believe sincerely that women should not be allowed to go to school, and others that homosexuals should be killed, and maybe their beliefs and their souls are not evil but it's what you do that matters. Faith does not give them the right to invade other people's lives and cause them harm.
We're talking here about the public humiliation (and consequential harassment and threats that anyone but an utter and abject idiot should expect to be a consequence) by a person who has no qualification and no cause other than her debatable faith. Sbe did the wrong thing to the wrong person in the wrong way for the wrong reason. Evil is as evil does. Her beliefs might not be evil, but she is.
You say elsewhere that you're on her side. Does that mean you believe it should be her privilege or her right to demand to challenge publicly the biological sex of any person who fails to meet her standards of girlishness? Does it mean, as her behavior suggests, that the default position of anyone she chooses must be to be presumed transgender until proven otherwise?
I sure hope I never wake up in the hate filled, tyrannical and prurient world you seem to hope for.