The purpose of the suspension was irrelevant. The military officers declaring the suspension could not be lawfully delegated such authority. The action was unlawful.
Even Mario Cuomo has a handle on this one.
The writ of habeas corpus is one of the fundamental constitutional guarantees of personal liberty, assuring a person detained by the government an opporutnity to challenge the detention before a court or judge. There is no question that Lincoln took it upon himself to authorize suspending the writ in contradiction of the Constitution as interpreted by the Supreme Court. He also suppressed two established newspapers, provided unappropriated funds for the purchase of military equipment, allowed a military tribunal to convict Maryland civilian John Merryman without bringing specific charges (to the horror of the still-reigning, eighty-five-year-old Chief Justice Roger B. Taney), and even signed the first income tax act, all in apparent violation of the law.
Source: Mario Cuomo, Why Lincoln Matters, 2004, p. 76-7.
Notwithstanding, however, Lincoln's clever attempts at exculpation, or at least mitigation, and his advocates' pleas for understanding the dire circumstances he faced, I still wish that the great Lincoln had stood by the Constitution despite the strong temptatin not to. Our government has ample authority under the Constitution to take those steps that are genuinely necessary for our security. At the same time, our system demands that government act only on the basis of measures that have been the subject of open and thoughtful debate in Congress and among the American people and that invasions of the liberty or equal dignity of any individual are subject to review by courts that are open to those affected and independent of the government that is curtailing freedom.Lincoln's willingness to put himself above the law was particularly unfortunate because of the strong pledge to constitutional fidelity he had made and affirmed in his earlier days. In his Lyceum speech of 1838 he went so far as to say that compliance with the letter and the spirit of the law should be treated as the "political religion" of the nation.
Source: Mario Cuomo, Why Lincoln Matters, 2004, p. 85.
CUOMO on Lincoln and Free Speech
Lincoln had a way of personalizing even the most abstract arguments, a talent that made his explanations both palatable and unforgettable. Defending his broad use of executive authority to the Albany opposition in 1863, he selected a vivid example, asking:
Must I shoot a simple-minded soldier boy who deserts, while I must not touch a hair of a wiley [sic] agitator who induces him to desert? This is none the less injurious when effected by getting a father, or brother, or friend, into a public meeting, and there working upon his feelings, till he is persuaded to write the soldier boy, that he is fighting in a bad cause, for a wicked administration of a contemptable government too weak to arrest and punish him if he shall desert, I think that in such a case, to silence the agitator, and save the boy, is not only constitutional, but, withal, a great mercy. [53]
Of course what Lincoln was saying, as touching as it sounds, might be translated into something like this: If the government thinks a war is a good idea but a citizen thinks it is an abomination and a fraud, he is not free to say so because he might convince someone.
[53] Collected Works, 6:266-67.
Source: Mario Cuomo, Why Lincoln Matters, 2004, p. 82
It's called the "chain of command." You, of all people, should know that.
What Lincoln was really saying was, "If you attempt to illegally subvert the war effort, you might end up in the graybar hotel."
As John Merryman was Taney's Baltimore neighbor and acquaintance, and that there were other judges that could have considered the habeas petition, Taney certainly could have recused himself. He chose confrontation because he was a pro-southern activist justice.
Assuming that Lincoln's exercise of emergency warpowers and suspension of (the privilege of the writ of) habeas corpus were constitutional, then, as Farber points out in Lincoln's Constitution (pg 190-191), the court would have utterly lacked jurisdiction to hear a habeas petition. After Congress retrospectively approved Lincoln's actions, Taney's pique in Ex parte Merryman became a moot point.
Farber writes (pg 162), "Although it is usually said that the Supreme Court never ruled on the legality of Lincoln's habeas suspension, Moyer [v Peabody] was the next best thing to a direct holding on the point, though delivered years after the fact. In the spring and summer of 1861, the area of isurrection might be said to include Maryland. If so, under Moyer, Lincoln clearly would have been empowered to use deadly force to suppress insurrection. It is hard to quarrel with [Oliver Wendell] Holmes's conclusion that the power to detain dangerous individuals goes along with the power to use deadly military force against them."