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Not sure why this split would be a problem? It's a very Big Social Media idea that everyone should use the same thing and expose themselves / be exposed to everything.
This has been a function of societies for as long as societies have existed, and addressing it requires honest reflection. In this case: "why is there such a huge overlap between people competent and willing to host federated social media servers, and people who don't want to be around me?"
Unfortunately there is a pervasive attitude amongst a certain personality type, that if someone criticizes them, then that someone must be wrong, and must be fought, no matter what. It's common enough to have ICD-10 diagnosis codes for it: Narcissistic Personality Disorder and/or Oppositional Defiant Disorder.
This is why I rarely try to change people's minds anymore unless they appear receptive to it: there's a good chance an overactive amygdala will see it as an attack and just make more work for me, wasting my time. It's easier to just talk to them about something else, or if they're being unnecessarily rude to people: not talk to them.
You might reflect upon your own short comment history (or your username) and judge for yourself what proportion is polite & respectful vs. rude & belligerent, and consequently whether the average person would want to try having a nice conversation with you.
Or they disagree with your views so intensely that they want you silenced.
That's what happened with https://spinster.xyz defederation. A group of male administrators of other Fediverse instances took umbrage at the women-centered, feminist discussion there and between them defederated hundreds of servers away from Spinster.
This was on top of misogynistic attacks and attempts to deplatform. Some unfortunately successful, like the removal of the Spinster app from the Google Play Store and F-Droid.
You're referring to an instance in which nobody was silenced, and all that happened was that some people chose not to interact with other people. That's totally okay! You don't have to interact with folks you think are insufferable.
> This was on top of misogynistic attacks
Unfortunately, most social networks are full of misogynists, racists, etc. As the size of the network grows, the probability of it including a jerk approaches 100%. In fact, this is one of the reasons someone might choose to run their own network in which they don't have to associate with said jerks. Based on a cursory search of your example, it looks like a lot of folks felt that spinster.xyz wasn't worth voluntarily associating with, perhaps because there was a high proportions of jerks.