This sluggardly realization on my part was partly the result of this topic's never having been really discussed in the traditional accounts. Certainly I'd never seen the implications discussed, although my father, who was a Civil War buff after his own generation's fashion (he read Catton and Sandburg), probably will not have let the implications escape him.
My dad was a Unionist, being an Indiana man conscious that his ancestors had served in both the Union Army and Navy (one man, a Timothy Radigan, was wounded in the hand in some engagement or other; the hand becoming gangrenous, the Union medicoes applied the bluebottle cure, which was described to me in some detail, including Radigan's personal recollection of the strange sensation of having bluebottle larvae crawling around in his hand, cleaning up his gangrene problem and saving his hand), and so he won't have made a big deal out of it, but he will have noticed -- not many things like that escaped him. He was, after all, a prosecutor's son and had the gift (when he went out dressed in his long tweed coat and leather gloves, people would ask him if he were an FBI agent -- just because he came across that way), and if the Massachusetts Fourth and Sixth Regiments were ready to deploy south on the day of Lincoln's proclamation and call, the Old Man will have noticed that. And he knew all about the suspension of habeas -- I remember his mentioning it to me, and his dimming view of some of Lincoln's war measures, although I wasn't yet old enough to engage the subject beyond a boy's level of interest in the Civil War.
But, if a State may lawfully go out of the Union, having done so, it may also discard the republican form of government; so that to prevent its going out, is an indispensable means, to the end, of maintaining the guaranty mentioned; and when an end is lawful and obligatory, the indispensable means to it, are also lawful, and obligatory."
This is one of the clearest statements of "the end justifies the means" I've ever seen. And I would call our interlocutors' attention to it, to notice that he privileged ends above means (he was, after all, a Rational personality, in the language of Myers-Briggs). I've made the same argument about his advocacy of abolition and the Civil War which accomplished it: that abolition being IMHO Lincoln's end, then the Civil War is understandable as his means. He was at some pains to disguise his purpose in his public speeches during the 1860 campaign, but his private papers from the mid-1850's published by David Donald and others discover his fixation on slavery as The Problem, and so it is not unreasonable to conclude that he finally decided that a military, extraconstitutional solution was the only viable road to abolition.
If that intermediate goal is recognized, of curing "the slavery problem" with a hot poker, then it is possible to trace the outlines of his slow, steady course of baiting the Southerners to violence (the same strategy followed by Martin Luther King, by the way), to give himself the pretext for war, while shoving its onus, as he himself declared in the First Inaugural, onto his intended victims. The same steady progress to war, moreover, that was noticed and thoroughly approved of, even if he didn't perhaps grasp his principal's full arc of intention, by John Nicolay, whom I have quoted above.
Not only did Lincoln not quote the rest of the clause, as you pointed out, he also "slid in" the imputation, the insinuation that the guarantee that he spoke about, of a "republican form of government", would be broken by the Southern States, i.e. that they would abandon republican government and immediately become something completely different, which insinuation is an operational lie. None of the Southern States abandoned republicanism, and in fact were better conservators of it than the North -- a point that, in the passages you quoted, even James McPherson concedes. Lincoln's insinuation that they would, was a convenient fiction that covered operative violence on the spirit of the Constitution -- which still bound him, if it didn't bind the States that had withdrawn from it.
Contrary Lincoln, the Southern States kept the Consitution better than he did, who said he was defending it, but was in fact trampling it.