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Yes, very much feels like governing bodies are on the wrong side of history here. If we accept that there are protected categories (as we do for weight classes in various sports) then we accept some set of arbitrary rules that define these protected categories. The tricky thing is identifying which arbitrary categories to protect and I don’t have a coherent view on that and I’m not sure that there is any solution that won’t unfairly exclude some group of people. However, whatever the arbitrary categories are, the governing bodies must do more to ensure that their enforcement is conducted in a sensitive and humane way.
Regarding how these females' are being treated this is worth a read.
https://www.washingtonpost.com/lifestyle/style/we-celebrated-michael-phelpss-genetic-differences-why-punish-caster-semenya-for-hers/2019/05/02/93d08c8c-6c2b-11e9-be3a-33217240a539_story.html