If a King said "off with his head", and someone carried out that order in a country where this was illegal, who did wrong? Is the King simply exercising his rights to free speech? What about paedophiles sharing images?
I suspect that it comes down to power imbalances. And that is something difficult to measure. A dictator and an influencer both have power to cause a lot of harm in what they say, as does an adult who shouldn't be near a child.
I agree with your example of the atheist, and in fact that has been the case for hundreds of years. The 'harm' in that case is something that people disagree on. An atheist and most scientists would disagree in the harm caused in that situation.