Greater gender equality isn't going to break the underlying themes or point of 40K. You can have a thoroughly awful and dystopian society with at least ostensible gender equality (q.v. Stalinist Soviet Union). EDIT: And really a lot of the Empire already seems pretty equal in this regard - Imperial Guard, the secret police, the Imperial bureaucracy, etc.
A "cold war" policy towards the xenos rather than outright extermination is a bit more of a stretch but really, play it like Rokugan in L5R - only certain individuals are authorized to deal with the xenos and we certainly don't want xenos wandering around the Empire freely (which in many ways reflects what is already the case in Rogue Trader) - and you still have a shitsack setting that's pretty much doomed to fall to Chaos anyway. Especially when there'll be plenty of people - both those serving Chaos and those in various governments - eager to start up the next "hot war" at any given time. Again, I don't see how this misses the point of 40K.
Caveat: I'm an RPG guy, not a wargame guy, so I err on the side of "what will let me run a more interesting campaign" rather than "there must be ONLY WAR so that we can sell more minis".
Wasn't there pretty much a cannonical thing from even GW that women turned into men when they joined Space Marines due to the whole genetic playing thing? Should sit well with all the genderfluid crowds.
I've never encountered that in canon (not that I've read every last GW book, o'course) and I suspect that if GW
had stated that canonically, it would have shown up in at least one of the "female Space marines" threads - certainly some folks make that argument, but I've never seen a GW statement to that effect.
That said, pretty sure the leaders of Adeptus probably care fuck and all about who's dying for the Imperium, as long as the machinery keeps on grinding and they can live cosy lives in bunkers of Terra.
The clue is in "Fascist", really.
And that, too.