Let's repeat what you cite the Supreme Court as saying:
"the whole executive power resides with the president."
That is executive, not legislative.
"Under the constitution of the United States, congress is the only power which can authorize the suspension of the privilege of the writ." Ex Parte Merryman, 1861. Issued at the Supreme Court as an in chambers opinion of the Chief Justice of the Supreme Court.
Lincoln noted in his July 4, 1861 message to Congress that, "Now it is insisted that Congress, and not the Executive, is vested with this power." He artfully avoided mentioning that it was so insisted by the Chief Justice of the Supreme Court in Ex Parte Merryman.
[Walt] The question of whether the president may or may not suspend the writ has not been answered to this very day.
"Under the constitution of the United States, congress is the only power which can authorize the suspension of the privilege of the writ." Ex Parte Merryman, 1861. Issued at the Supreme Court as an in chambers opinion of the Chief Justice of the Supreme Court.
The question was answered by CJ Taney writing as the Chief Justice of the Supreme Court. Lincoln did not like the answer and chose to violate the law.
The sure way to put the kibosh on President Lincoln suspending the Writ was to get the issue before the whole Court. Taney didn't push that because his Merryman ruling, like Dred Scott was poorly based in the law.
"Scholars still debate whether Lincoln had the authority to invoke the Constitutional provision suspending Habeas Corpus during the early days of the war. I will not wade into the muddy waters of that debate. I am more interested in talking about what Lincoln did after March of 1863--for that is when Congress gave Lincoln legislative authority to suspend the writ. From that point forward, Lincoln faced no constitutional obstacles. He could arrest whomever he chose, without courts interfering with Writs of Habeas Corpus. What did Lincoln do at this point? Did he attempt to stifle political debate, by imprisoning his opponents? In short, did he trample on the civil liberties the Writ of Habeas Corpus was meant to protect?
A recent historical study, entitled The Fate of Liberty, says "no." The author, Mark Neely, combed through the musty boxes of arrest records from the Civil War "to find out who was arrested when the Writ of Habeas Corpus was suspended and why." Neely concludes that, throughout the war, Lincoln was guided by a "steady desire to avoid political abuse under the Habeas-Corpus policy."
According to the best estimates, about 38,000 civilians were arrested by the military during the Civil War. Who were they? Almost all fell within a few categories: "draft dodgers, suspected deserters, defrauders of the government, swindlers of recruits, ex-Confederate soldiers, and smugglers." And strikingly, most of these were Confederate citizens, caught behind Northern lines. The numbers show that very few civilians were taken from their homes and arrested. And of those few arrests, only a handful were colored by political considerations.
Indeed, Lincoln issued his most sweeping proclamation suspending Habeas Corpus not to silence political dissent, but to stop judicial interference in the draft. Early in the war, patriotic zeal was so strong that volunteers flooded into the Army. But as the war dragged on, public enthusiasm ebbed. Eventually, the government was reduced to instituting a draft. Conscription was rather unpopular, to say the least. If any of you remember the burning of draft cards during the Vietnam War, imagine that unrest multiplied several times over in the New York City Draft Riots in 1863. The problem was especially bad in Pennsylvania. Coal miners attacked men thought to be "in sympathy with the draft." State and federal courts added to the problem. They were churning out Writs of Habeas Corpus, freeing soldiers as soon as they were drafted. Lincoln observed that "[T]he course pursued by certain judges is defeating the draft."
Lincoln's response was to suspend the Writ throughout the North in any case that involved military arrest of deserters or draft dodgers. And for good measure, he threw in prisoners of war, spies, and those giving assistance to the enemy--say, by smuggling goods to the Confederate government. But his focus was always on military necessity. Lincoln never tried to suppress political dissent. He understood that a democracy only grows stronger by allowing people to voice their opposition to the government, even in the midst of war. He understood that the strength of the Union lay not only in force of arms, but in the liberties that were guaranteed by the open, and sometimes heated, exchange of ideas. And as one historian has put it, "[T]he opposition press in the North was vibrant, vigorous, and often vicious."
...
In sum, the Vallandigham episode is emblematic of Lincoln's approach to political liberties during the Civil War. The President was not out to trample on the First Amendment. He was not out to crush his political opposition. He suspended the writ of Habeas Corpus in response to perceived military threats to the Union. After he, and later Congress, removed that Constitutional safeguard, the Lincoln Administration did not use its power selfishly or arbitrarily. It arrested only those people who actively supported the Confederate war machine--people like Merryman, who recruited troops to march south. And when people walked this fine line between political dissent and treason, as Vallandigham did, Lincoln tried to err on the side of free speech.
Midway through the war, Lincoln predicted that Habeas Corpus would quickly be re-instituted after the war was over. He could not bring himself to believe that Americans would allow the wartime suspension of Habeas Corpus to extend into peacetime, he said, "Any more than I am able to believe that a man could contract so strong an appetite for emetics during temporary illness as to persist in feeding upon them during the remainder of his healthful life." Lincoln died before he could see the writ of habeas corpus restored.
In one of his most famous debates with Stephen Douglas, Lincoln spoke about how a society that tolerates slavery corrodes the very foundations of its own liberty. These words, I think, reveal Lincoln's awareness that he wasn't battling for territory on a map. He was battling to preserve a nation "conceived in Liberty."
Lincoln asked:
"What constitutes the bulwark of our own liberty and independence? It is not our frowning battlements, our bristling sea coasts, the guns of our war steamers, or the strength of our gallant and disciplined army. These are not our reliance against a resumption of tyranny in our fair land. All of them may be turned against our liberties, without making us stronger or weaker for the struggle. Our reliance is in the love of liberty which God has planted in our bosoms. Our defense is in the preservation of the spirit which prizes liberty as the heritage of all men, in all lands, everywhere. Destroy this spirit, and you have planted the seeds of despotism around our doors. Familiarize yourselves with the chains of bondage, and you are preparing your own limbs to wear them. Accustomed to trample on the rights of those around you, you have lost the genius of your own independence, and become the fit subjects of the first cunning tyrant who rises."
So today, let us heed the wisdom of a man who led our nation to a "new birth of freedom." Let us always be, first and foremost, lovers of liberty. Thank you"
--Remarks of Justice Sandra Day O'Connor.
Walt