Mr. Jones responds to a historical fallacy (selectivity) with one closer to my heart: ahistoricality, or, to use the more technical term, presentism.* It's true that Lincoln's orders during the Civil War often violate our present sense of the rules and morals of war, and individual commanders carried out what can only be called atrocities without punishment or even uproar. But this is one situation where relativism is required: the ethics of war -- Hemingway said that war, no matter how justified, was a crime, but neither he nor I are actually pacifists in any meaningful sense -- have changed dramatically over the 20th century. In fact, there wasn't much "Law of War" in the mid-19th century, particularly in the context of civil rebellion: in theory, the North could have considered every southern soldier a traitor and shot them on sight; Geneva actually would protect against that now, at least for uniformed combatants. Now there is a substantial body of law, largely based on avoiding repeats of past atrocities, which should bind the President against torture (which is pretty well defined, unless you happen to be willfully ignorant or Alberto Gonzales), unaccountability ("ghost" detainees), arrest of minors, etc.
The relevant question is whether Lincoln's conduct of war was bounded by the conventions and laws of the time, whether he violated existing guidelines, whether he restrained his troops from committing atrocities which they might otherwise have committed, legally or otherwise. The Order that Mr. Jones cites was a remarkably advanced statement of principles for its time, and that made it unlikely that officers trained under less restrictive rules, or soldiers hastily assembled, would follow them clearly and consistently. That the statement was accompanied by the repeal of Habeus Corpus, which, as Mr. Jones notes, dramatically reduces Lincoln's stature as a paragon protector of rights and legal ethics, but given the nature of the war being fought, it's not incomparable to the USA PATRIOT act....
* There's also a bit of selectivity in Mr. Jones' limitation of discussion of Bush war policy to Abu Ghraib and interrogation technique.
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