I think you fail to understand the point of the Harper's letter. It is not about protecting the signatories or any particular individual or group, it's about protecting the open discussion of controversial ideas.

As a society, we need to be able to talk about ideas that may not be popular or comfortable in pursuit of the truth.

I want our public intellectuals, writers, journalists, politicians, entrepreneurs and scholars to be able to express themselves with complete freedom regardless of their race, gender, ethnicity, sexual orientation and economic status. I don't want them to be intimidated by the mob. I don't want them to self-censor to protect their livelihoods and reputations. And even if I despise the ideas they utter, I still want to protect their right and ability to express them without fear of retribution.

This is taken from Karl Popper's Paradox of Tolerance that you cite: “I do not imply for instance, that we should always suppress the utterance of intolerant philosophies; as long as we can counter them by rational argument and keep them in check by public opinion, suppression would be most unwise."