I am surprised that no previous answerer or commenter has pointed out that the sentence in question makes perfect sense if you read secure as a verb. That is, the sentence as written by Thoreau:
It has the ring of a saner sanity than an ordinary discipline and habits of life, than an ordinary organization, secure.
could be read as meaning essentially the same thing as this sentence:
It has the ring of a saner sanity than one can secure for oneself through [dedication to] an ordinary discipline and [ordinary] habits of life, [and] than one might secure through an ordinary organization [of one's life].
The only difference in sense that I see between this second version of the sentence and Thoreau's original is that in the original wording, "discipline," "habits," and "organization" are the active agents that secure one's sanity (albeit a less sane sanity than John Brown possesses, according to Thoreau), whereas in my rewording, one [that is a person] is the active agent that secures one's garden-variety sanity—which one accomplishes by means of ordinary discipline, ordinary habits of life, and ordinary organization.
I can't claim that my rewording uses secure in the way that Thoreau intended—because I am not sure what Thoreau meant to say—but I can and do claim that such a reading makes sense. The fact that secure (if it is being used as a verb) appears in plural form merely signals that Thoreau is implicitly combining "than an ordinary discipline and habits of life [and] than an ordinary organization" to build a plural subject for the verb.