I think her going has nothing to do with Equalities let alone the GRA.
This is Boris thinking it is outrageous that a woman should be Defence Secretary. Heavens knows what gung ho idiot Boris will appoint in her place. Prepare for Premier Boris banging the drum for another gulf war or something to distract us from the fact Brexit will be a fuck up.
It seems to me, despite commentators saying TM was committed to women's rights nobody actually wanted to be Women and Equalities Minister.
So it will just get palmed off on someone else who just doesn't care and will easily given in the well established entrenched trans network in Parliament.
And suspect that 99.9% of the population are equally indifferent.
