While the rollback of post Civil War reconstruction and tolerance of violent segregationists is definitely an instance of "tolerance of the intolerant", you should read the article and source material it's quoting more closely, because you're contradicting the entire argument they're making. Here's the quoted passage again, but in full

[Less well known is the paradox of tolerance: Unlimited tolerance must lead to the disappearance of tolerance. If we extend unlimited tolerance even to those who are intolerant, if we are not prepared to defend a tolerant society against the onslaught of the intolerant, then the tolerant will be destroyed, and tolerance with them.—In this formulation, 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 certainly be most unwise.] But we should claim the right to suppress them [intolerant ideologies] if necessary even by force; for it may easily turn out that they are not prepared to meet us on the level of rational argument, but begin by denouncing all argument; they may forbid their followers to listen to rational argument, because it is deceptive, and teach them to answer arguments by the use of their fists or pistols.

As usual in political philosophy, the definition of intolerance is stricter and includes an element of rejection by force or imposition. From the passage, the type of intolerance they refer to is the kind that uses force and refuses debate. They even explicitly reject that we should in general "suppress the utterance of intolerant philosophies" as long as rational argument & public opinion still govern public choice.

In that discourse where the philosopher is arguing that a free, open inquiry and rational argument is crucial to an open society, they unsurprising aren't arguing for the suppression of exclusionary opinions. They're arguing for a system of governance that protects freedom of individuals to debate (and denounce) each other.

So, tolerating segregationist terrorists in the post Civil War is a case of "extend unlimited tolerance even to those who are intolerant" as mentioned in the paradox. In contrast, a disagreement with someone who is not imposing their beliefs is not, and the paradox has no bearing.

Paradox of tolerance has no bearing on disagreements lacking imposition, and is used to defend open discourse, not argue against it.