You see, during Southern "Reconstruction" [I put it in quotations because it's a word the does not really fit], the defeated Southerner's had no real legal recourse against any Yankee (dare I say?) tyranny. Now that is not to justify any of the unlawful (using the word "lawful" in a biblical sense) things that the Southerner's may have done; I'm just pointing out that the South had no legal recourse, so it is quite natural that the "law" would end up being tyrannical (from both directions) and of the vigilante sort.
But to come back to the point at hand--because former Confederates were not, under Radical Republican "Reconstruction", citizens of the United States (we will not discuss the legality of secession here as that would bog us down), they had none of the rights granted citizens under the Constitution. On top of that, their states were under Marital Law which, as far as I can tell, seems to suspend (at least in this case) normal judicial activity. Taking all that into account, they could be pressed and squeezed and mistreated without being able to protect themselves through legal channels. (By the way, I'm not saying all the Yankee's were as hard-hearted and cruel as, say, Thaddeus Stevens...)
This was sure to pose a quandary to many a gallant soldier. What was he to do to protect (again) his home and family and way of life?
I am sure many wished heartily to take up arms yet again. Indeed, the beloved general of the South, Robert E. Lee himself remarked that if he had known what Reconstruction would be, he never would have surrendered--and you probably know that General Lee was one of the strongest advocates of living at and in peace with the northern portion of the country. But--that was not an option (here is that word again) legally (which is probably one of the reasons it didn't happen).
Well, let's return back to our theology for the answer to that question. (I wish I had my notes from Calvin's Institutes handy! I will try to roughly exposit my remembrances of what he said.)
First--governments are granted their authority by God (one of three jurisdictions). Therefore, they are to be obeyed in as far as obedience does not mean disobedience to God.
Second--because governments are ordained by God, a citizen's lone, arbitrary disregarding of them (could call this anarchy), is wrong.
Third--in the Republican form of government (based actually upon the Presbyterian governmental form [King George recognized this in the war of 1776]), there are differing levels of governmental authority, besides being the different branches (judicial, legislative, and executive). One governmental layer down holds (or can hold) the next one up accountable. (They should.) Therefore, legally, a lesser magistrate only can lead what would be called a 'rebellion' against the state.
Now, going back to our original topic--any armed resistance on the part of the defeated South against the Yankee tyrant would have been unbiblical in the sense that there was no legal, lesser magistrate to lead it. Beside, to be entirely pragmatic...I doubt it would have done much good because the manpower of the South was drastically reduced, they had no money, or means of arming, equipping, and supporting men on the field. But that is not the point, the point is, being without legal recourse, because they had been stripped (I would argue, unconstitutionally) of their citizenship they had no lesser magistrates (and to begin with, the ones they did have were simply Radical stooges) and therefore, no representation. (And I think I sorta did one of those logical jump thingys that I cannot remember the name of right there.)
And those are my 'putting-clean-sheets-on-the-bed' rambles (expanded). Forgive me if there are gaps in the thought process...or something. The subject is huge and expansive and I myself have barely scratched the surface of it. But...my mind does go down these channels and I have to write them down to solidify them in an at lease semi-articulate fashion.