There's no reason anyone who is confused should be disciplined. Confusion would be natural.
Shock and surprise would also be natural reactions. We are humans after all, and gender transformation is a complicated thing.
As far as toilets go, I think that one is pretty simple. genitals would dictate which toilet they use, the same as non trans people. Penis=little boys room,vagina = little girls room.
What about if he had both. Then he could really go fuck himself.