Guerilla wars don't need a lot to go on. An insurgency just needs some weapons and hit and run tactics to make life miserable. Look at Afghanistan.
If Lee had told everyone to go into the hills, they don't need a lot of "leadership" to continue the struggle.
What Lincoln would have done is up for debate. He did want to be generous to the South...which included not executing folks. You may not believe this but when he was first assassinated the Radical Republicans actually expected Johnson to be tougher on the South than Lincoln and thought it may have been a blessing in disguise than Lincoln was gone. He wanted Reconstruction to be as painless as possible, so a plan along Johnson's lines isn't as far fetched as people want to believe. I remember my history professor in college (who was very pro-Lincoln btw) argued the the best thing to happen to Lincoln's presidency was to die at the height of his powers right as the war ended. His point was that Reconstruction was probably always going to have issues and could have ended in disaster in about a thousand different ways, but as a martyr everyone would always assume Lincoln would have figured it out.
And once again, as stated earlier, there was a big, big worry that they Confederates would be found not guilty in a secession trial. This is the letter sent to President Johnson by Richard Henry Dana, Jr., who was sort of a Special Prosecutor that was to try any Confederates if the government went in that direction (Jefferson Davis was in jail for quite awhile and nearly died waiting trial, which obviously never happened). Dana wrote to Johnson indicating he had great misgivings about going to trial.
Letter was as follows
Sir,
While preparing with yourself, before you assumed your present post, to perform the honorable duty the President had assigned to us, of conducting the trial of Jefferson Davis, you know how much my mind was moved, from the first, by doubts of the expediency of trying him at all. The reasons which prevented my presenting those doubts no longer exist, and they have so ripened into conviction that I feel it my duty to lay them before you in form, as you now hold a post of official responsibly for the proceeding.
After the most serious reflection, I cannot see any good reason why the Government should make a question whether the late civil war was treason, and whether Jefferson Davis took any part in it, and submit those questions to the decision of a petit jury of the vicinage of Richmond at _nisi prius_ [“the first court to try Davis”].
As the Constitution in terms settles the fact that our republic is a state against which treason may be committed, the only constitutional question attending the late war was whether a levying of war against the United States which would otherwise be treason, is relieved of that character by the fact that it took the form of secession from the Union by state authority. In other words the legal issue was, whether secession by a State is a right, making an act legal and obligatory upon the nation which would otherwise have been treason.
This issue I suppose to have been settled by the action of every department of the Government, by the action of the people itself, and by those events which are definitive in the affairs of men.
The Supreme Court in the Prize Causes held, by happily a unanimous opinion, that acts of the States, whether secession ordinances, or in whatever form cast, could not be brought into the cases, as justifications for the war, and had no legal effect on the character of the war, or on the political status of territory or persons or property, and that the line of enemy's territory was a question of fact, depending upon the line of bayonets of an actual war. The rule in the Prize Causes has been steadily followed in the Supreme Court since, and in the Circuit Courts, without an intimation of a doubt. That the law making and executive departments have treated this secession and war as treason, is matter of history, as well as is the action of the people in the highest sanction of war.
It cannot be doubted that the Circuit Court at the trial will instruct the jury, in conformity with these decisions, that the late attempt to establish and sustain by war an independent empire within the United States was treason. The only question of fact submitted to the Jury will be whether Jefferson Davis took any part in the war. As it is one of the great facts of history that he was its head, civil and military, why should we desire to make a question of it and refer its decision to a jury, with power to find in the negative or affirmative, or to disagree? It is not an appropriate question for the decision of a jury; certainly it is not a fact which a Government should, without great cause, give a jury a chance to ignore.
We know that these indictments are to be tried in what was for five years enemy's territory, which is not yet restored to the exercise of all its political functions, and where the fires are not extinct. We know that it only requires one dissentient juror to defeat the Government and give Jefferson Davis and his favorers a triumph. Now, is not such a result one which we must include in our calculation of possibilities? Whatever modes may be legally adopted to draw a jury, or to purge it, and whatever the influence of the court or of counsel, we know that a favorer of treason may get upon the jury. But that is not necessary. A fear of personal violence or social ostracism may be enough to induce one man to withhold his assent from the verdict, especially as be need not come forward personally, nor give a reason, even in the jury-room.
This possible result would be most humiliating to the Government and people of this country, and none the less so from the fact that it would be absurd. The Government would be stopped in its judicial course because it could neither assume nor judicially determine that Jefferson Davis took part in the late civil war. Such a result would also bring into doubt the adequacy of our penal system to deal with such cases as this.
If it were important to secure a verdict as a means of punishing the defendant, the question would present itself differently. But it would be beneath the dignity of the Government and of the issue, to inflict upon him a minor punishment; and, as to a sentence of death, I am sure that, after this lapse of time and after all that has occurred in the interval, the people of the United States would not desire to see it enforced.
In fine, after the fullest consideration, it seems to me that, by pursuing the trial, the Government can get only a re-affirmation by a Circuit Court at _nisi prius_ of a rule of public law settled for this country in every way in which such a matter can be settled, only giving to a jury drawn from the region of the rebellion a chance to disregard the law when announced. It gives that jury a like opportunity to ignore the fact that Jefferson Davis took any part in the late civil war. And one man upon the jury can secure these results. The risks of such absurd and discreditable issues of a great state trial are assumed for the sake of a verdict which, if obtained, will settle nothing in law or national practice not now settled, and nothing in fact not now history, while no judgment rendered thereon do we think will be ever executed.
Besides these reasons, and perhaps because of them, I think that the public interest in the trial has ceased among the most earnest and loyal citizens.
If your views and those of the President should be in favor of proceeding with the trial, I am confident that I can do my duty as counsel, to the utmost of my ability and with all zeal. For my doubts are not what the verdict ought to be. On the contrary, I should feel all the more strongly, if the trial is begun, the importance of a victory to the Government, and the necessity of putting forth all powers and using all lawful means to secure it. Still, I feel it my duty to say that if the President should judge otherwise, my position in the cause is at his disposal.
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