This gets even more complicated philosophically, because it is often considered to be unconscionable for one group to force its views and ideals onto another group, because this destroys one of the groups, and diminishes the spectrum of the human condition.
Disclaimer: I haven't read beyond this post, so I'm sorry if someone beat me to this...
But Wierd, you answered your own question right here.
Fundamental human rights (in theory as I understand them) are those which prevent humans from from forcing their views and ideals on others or subjecting them to unjustified violence and suffering.
The problem with your use of the concept of group autonomy is that no group is isolated enough to practice their own prejudices in concrete action, without also forcing their views and ideals on other groups or subjecting them to unjustified violence and suffering. As society becomes more complex and integrated, it becomes more essential for exactly those reasons you are expressing concern over to discourage or eliminate actions rooted in prejudice.
Can you frame this in such a way that the immediate steps taken appear hypocritical? Sure. But that's easily done with just about any issue. It's not hypocritical if you take a broader view of the ultimate goals and effects as related to the principles in question.
Edit:
Ok... I see there was already a really drawn out and unchill argument for about two pages... I knew there were some posts, but didn't know it had already gone that far when I made this one. So sorry if I'm causing it to flare up further...
And I'd just like to add anyway that within the framing that accuses progressivism of hypocrisy, it is logically impossible for anyone to have any stance on the issue without engaging in that same definition of hyprocrisy. So the accusation is rendered completely meaningless, in my opinion.
"You're forcing your views on me by not allowing me to force my views on others, and that's wrong because people shouldn't force their views on each other."
Even if your goal is to allow individual cultures to flourish independently by creating more clearly defined spaces for them to operate how they please, that's still what the whole argument boils down to, when the primary features of those cultures that you (wierd) are suggesting deserves protection is their hostility towards other specific cultures and life choices. It's all hypocrisy and absurdity when reduced, so I lean towards whichever side of the absurdity causes the least actual victimization of individuals.