There is some potentially useful discussion going on at this thread about the issues with children understanding transgenderism that could be relevant for responding to the guidance.
Page 9 | My son can tell... | Mumsnet
For me, the guidance is as much (if not more) about the whole school population, teachers included, as it is about the few confused children who are seeking adjustments to be made for them in school.
One particularly useful comment (IMO) from the thread is as follows, with thanks to @akkakk
"...is that not of itself an indication as to how serious this has become that a child who speaks the truth could be punished or 'face a world of hurt'
the only we that we will keep truth central to our society is for all decent people to defend it...
and no, that doesn't mean that the trans community are not decent people - there will always be people who 'feel' more masculine or 'feminine', who feel body dysphoria, who are confused over what they really are - they are the community we should support and help to live a great life - ideally society should be helping them to come to terms with that disconnect and find ways to live as the sex they were born but the shape of man or woman they want to be...
that is totally different to those who impose this on the rest of society, who threaten, degrade and impose on others - none of that is part of a 'decent society' we need to stand up against lies and mis-truths, against those who twist words, change meanings, who gaslight and threaten, who pervert decency and corrupt others, those who abuse and minimise their actions...
if you have a boy who claims to be a girl - that is not the truth, they can't be, never can be, so someone else referring to them as a boy is simply speaking the truth and we must support and enable that in schools, media and society generally.
If you have a teacher who is male but pretending to be female, that is not living a truth - it is a safeguarding issue, and while there may be accommodations to allow it to take place, any comeback on pupils who refer to them truthfully as male is a step too far
so yes, there may be a 'world of hurt' but that is a threat -"if you don't join me in supporting / sharing / telling my lie to others I will make sure you face a world of hurt"- is that acceptable behaviour from e.g. a teacher? Surely any teacher who said anything like that in any other way would be instantly suspended and face disciplinary charges - we must not have dual standards...
so yes - that may be the outcome, but we should not shy away from the truth and the more that adults tell children the truth and support them in the truth, the easier it will become - and the better society will be...