Lincoln and Lee

Yes. In Lincoln's famous June 12, 1863 letter to Erastus Corning where he asked "Must I shoot a simple-minded soldier boy who deserts, while I must not touch a hair of a wiley agitator who induces him to desert?" Lincoln also wrote the following (my bold):

Ours is a case of Rebellion---so called by the resolutions before me---in fact, a clear, flagrant, and gigantic case of Rebellion; and the provision of the constitution that ``The previlege of the writ of Habeas Corpus shall not be suspended, unless when in cases of Rebellion or Invasion, the public Safety may require it'' is the provision which specially applies to our present case. This provision plainly attests the understanding of those who made the constitution that ordinary courts of justice are inadequate to ``cases of Rebellion''---attests their purpose that in such cases, men [9] may be held in custody whom the courts acting on ordinary rules, would discharge. Habeas Corpus, does not discharge men who are proved to be guilty of defined crime; and its suspension is allowed by the constitution on purpose that, men may be arrested and held, who can not be proved to be guilty of defined crime, ``when, in cases of Rebellion or Invasion the public Safety may require it.'' This is precisely our present case---a case of Rebellion, wherein the public Safety does require the suspension. Indeed, arrests by process of courts, and arrests in cases of rebellion, do not proceed altogether upon the same basis. The former is directed at the small per centage of ordinary and continuous perpetration of crime; while the latter is directed at sudden and extensive uprisings against the government, which, at most, will succeed or fail, in no great length of time. In the latter case, arrests are made, not so much for what has been done, as for what probably would be done. The latter is more for the preventive, and less for the vindictive, than the former. In such cases the purposes of men are much more easily understood, than in cases of ordinary crime. The man who stands by and says nothing, when the peril of his government is discussed, can not be misunderstood. If not hindered, he is sure to help the enemy. Much more, if he talks ambiguously---talks for his country with ``buts'' and ``ifs'' and ``ands.'' Of how little value the constitutional provision I have quoted will be rendered, if arrests shall never be made until defined crimes shall have been committed, may be illustrated by a few notable examples. Gen. John C. Breckienridge, Gen. Robert E. Lee, Gen. Joseph E. Johnston, Gen. John B. Magruder, Gen. William B. Preston, Gen. Simon B. Buckner, and Comodore [Franklin] Buchanan, now occupying the very highest places in the rebel war service, were all within the power of the government since the rebellion began, and were nearly as well known to be traitors then as now. Unquestionably if we had seized and held them, the insurgent cause would be much weaker. But no one of them had then committed any crime defined in the law. Every one of them if arrested would have been discharged on Habeas Corpus, were the writ allowed to operate. In view of these and similar cases, I think the time not unlikely to come when I shall be blamed for having made too few arrests rather than too many.
Collected Works of Abraham Lincoln Volume 6
 
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