We might be overthinking the problem by trying to reach some unattainable "golden" level of correct morality.
Society has a way of balancing out its norms on its own. There are always conservative (or let's say "intolerant") ideas and more progressive, or tolerant, ones vying for acceptance in public opinion. We have seen that a "we've always done it that way" attitude has given way to more important concerns regarding equality when it comes to issues of race. We've also seen more libertarian, "go with the flow" attitudes muted by conservative ideas in regard to things like nudism, incest, bestiality, polygamy.
Generally we've gone on a path toward progress in the last century that has had positive effects. Hopefuly we will continue on this path; if we err, we can probably correct ourselves.
Of course when talking about this kind of "free market" of ideas, we have to make the same kind of assumptions we make when dealing with economic markets. To that end, I believe that what we "should" do is to ensure that we are rational actors, making decisions for logical reasons; that we have good information; that no one group has an unreasonable grip on decision-making or public influence.
Beyond these considerations, I don't think we can make normative judgments on "tolerance" or "intolerance" as a whole (which is the problem that was encountered in the original post.) These things have to be considered on a case-by-case basis.
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