The phrase "paradox of tolerance" is almost never used correctly; it's usually used to justify the stifling of speech, rather than the prevention of violence.
Violent resistance to fascism is justified, but that doesn't mean violence is ever anything but a tragedy. Are you happy that the allies killed loads of axis fighters in ww2, or sad that it was necessary? Bloodlust never brings peace even if it's supposedly for a good cause.
Kirk's killer's political affiliations remain as ever a matter of speculation, so calling it "infighting" is at best wishful thinking.