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Saying "that's just the way things are" is no excuse for tolerating the sort of behavior under discussion here.

You're correct that it comes with the territory, but that doesn't absolve organizations (and governments) of writing and enforcing policies to mitigate the damage done by harassment. Nor should we excuse away an obligation to repudiate harassment when we encounter it. Saying it's status quo won't fix anything.

Regarding the John Stuart Mill quote above: I agree. It's not the views of the people in question that offend me, it's their alleged actions. Harassment is not free speech; it doesn't attack ideas, it attacks people.