The point being made in the guidance, is that pronouns are not a neutral act of kindness without consequence or wider impact, and that other children's interests have to be considered as of equal importance. And that this has long been presented as a truth and the only acceptable view, whereas those who do not agree and have other views are equally worthy of respect.
Yes, it's going to be uncomfortable to move things back to a more neutral place, but that more neutral place serves all children's interests more equally. To leave things where they currently are because it would be too upsetting to affect children who are gender questioning merely makes clear that within this ideology those children's feelings and impact matters but other children's don't. And continues to preserve the territory that has enabled schools to transition children behind parents' backs, and to help children down a path towards medicalisation that there is no knowing how many will come to regret and be seriously harmed by. The pronouns are an intrinsic part of the whole. They also play a large part in confusing children that they can change sex, and has enabled situations where children have been required to undress in the presence of a child of the opposite sex despite their discomfort because the pronouns enforced the illusion that this child was not of the sex they in fact were.
This muddle shouldn't have been allowed to happen, I completely agree. To work on undoing it now is better late than never.