Because that quote fundamentally discusses cases where pruning said noxious branch is a risk to non-noxious branches.
Sometimes you can just prune a noxious branch and that's that.
This quote is from the The Report of 1800 [1], where he goes on to say:
> Had “Sedition acts,” forbidding every publication that might bring the constituted agents into contempt or disrepute, or that might excite the hatred of the people against the authors of unjust or pernicious measures, been uniformly enforced against the press; might not the United States have been languishing at this day, under the infirmities of a sickly confederation? Might they not possibly be miserable colonies, groaning under a foreign yoke?
He’s crediting the formation of the United States to speech that was “noxious” to either the British parliament or the Confederate states in power at the time. This noxious speech was absolutely a risk to the extent that sedition acts were being threatened. He’s advocating freedom of the press even when their speech may excite hatred.
[1] https://founders.archives.gov/documents/Madison/01-17-02-020...
How is it unrelated? A noxious branch is exactly something that many or most people would consider abhorrent and perceive as not in good faith.
There will always be some moral veil put forth by censors to justify their actions. A good example is banning discussion on Ivermectin as a treatment for COVID. Some consider that a noxious branch — quackery endangering public health — but if it’s immediately pruned we won’t be able to see if it yields proper fruits.