I would treat this the same way we treated the relentless teaching of religion at my kids' schools. We tell them some people believe this stuff, that they can choose to believe this too if they want and that belief serves a number of purposes (some positive) for many people but that their mum and dad look to science for answers and that tells us this, this, this and this.
Which has meant that unlike me at their age the kids are very tolerant of religious beliefs but the one thing they understand above all is that they are free to disbelieve.
It also meant that when my kids got taught the doctrine of gender identity in school, they didn't believe it. Not that we knew this was coming, but when you have lively discussions about gender being socially constructed and imposed rather than innate, about biology, the limitations of modern medicine, about neurology etc it leads to kids looking at the gender wang with considerable scepticism.
Or view it as "bollocks" as my then 11-year old put it.
And yes, I agree, it can be stigmatising to be taken out of religious education. The kids asked us not to even though it would have been my preference.
But if you are comfortable talking to your children about how and why the doctrine of gender identity is no more or less than any other (religious) belief, you can counteract the indoctrination.
What you unfortunately cannot do, which we have been able to do with religious education until now is tell the kids that as long as they debate respectfully they can disagree with their teacher about any religious tenets of any faith.
But I grew up under a totalitarian regime, so managing the unsayable nature of dissent in regard to the doctrine of gender identity is a mere matter of remembering my childhood rules.
Never speak your mind in front of strangers. Never disagree with a person in authority in public. Never fall for the friendly inquiry. Never trust that your words won't be reported.
Fucking horrific that this is happening in a supposedly democratic state, but it is what it is. (If we're talking navigating this indoctrination in this climate in regard to the kids. If we're talking about resisting, that's a different matter.)