I think specific examples are needed to be able to take this further. I get the impression that you have certain cases in mind where discussion has been stifled, or somebody that challenged the consensus view was shouted down. But I don't know what those cases are, and the specifics matter so much that one can't really talk general principles.
Let me try an example of a case that I see. It used to be the medical consensus as well as the widespread common opinion that homosexuality was a mental illness, and that it could potentially be 'cured'. We have learned so much about this over the last fifty years, that hardly anybody holds that view any more and it is thoroughly rejected by all psychological and medical peak bodies. If anybody publicly argues that homosexuality is a mental illness in a developed country, they will most likely be roundly condemned.
Is that a good thing? I think it is. And the same applies to denial of the Nazi genocide of Jews or claims that people of African descent are less intelligent than those of European descent. While open public discussion is generally a good thing, we need to balance that against the harm that is done by publicly stating certain opinions. That does not mean one could not discuss those things privately, and I'm sure most of the small group that hold such opinions do so amongst themselves. To expand on JS Mill's example of free speech, it's the difference between shouting 'Fire' in a crowded theatre and quietly asking one's neighbour 'Do you smell smoke?'.
Let's bear in mind that the penalty for claiming that homosexual people are mentally ill is not burning at the stake, or even imprisonment. It is just social condemnation, and free speech principles are about legal punishment, not social condemnation. I would strongly oppose laws to criminalise denial of the the Nazi genocide despite my detestation of such denial, and most countries seem to share that opinion. Germany is a special case, for powerful historical reasons and, while I think their criminalisation of public denialism is unfortunate, I can understand why they consider it necessary.
Those three examples are easy cases. There are more difficult ones, of which I think abortion and marriage equality are examples. In both cases, some (not all!) activists on one side often portray those on the other as inhuman, hateful monsters. I think it is profoundly unhelpful to call opponents of marriage equality homophobic, or opponents of abortion on demand misogynistic. But human nature being what it is, that unfortunately happens in debates that people care so deeply about.
One thing philosophers can do is provide an example of the right way to publicly discuss these things. I particularly admire the way Peter Singer argues for abortion on demand calmly, rationally and compassionately, without demonising those that disagree with him, and despite the fact that those same people often demonise him, calling him a Nazi, a child-killer and worse. And I believe there are Christian philosophers on the other side of the debate that do the same (there's a name of one on the tip of my tongue, but it eludes me at present).