No it didn't. In fact, the properly elected and seated members of that government were prosecuted and penalized repeatedly and their authority overrun by military coercion with the sanction of Lincoln. Lincoln unilaterally and unconstitutionally suspended habeas corpus almost immediately after the war broke out and used it to silence both his critics and those who acted to impede his waging of war. Properly elected members of the Maryland legislature were imprisoned and others were sent fleeing from Annapolis under threat of having the same done to them.
One of the worst cases happened in Missouri, which, at the opening of the war, had decided to remain in the union and declared its neutrality in the conflict like Kentucky. The Missouri government called out its state militia at the beginning of the war and stationed them in St. Louis with the task of keeping the arsenals from being taken for use in warfare on their soil. Lincoln's army crossed into the state, violated its neutrality, captured the militia, and marched them through St. Louis as prisoners. When civilians came out to the streets in protest, the army opened fire on them killing several. This incited the Missouri legislature, which had previously voted NOT to secede, to organize troops in opposition to Lincoln's violation of their neutrality. The feds responded by marching the U.S. army on the state capital to oust the governor and state legislature!!! As the state militia organized to hold off the army, the legislature and governor fled the capital toward Arkansas. The state government convened in October in the town of Neosho, where the previously neutral legislature that had decided earlier not to secede drafted an emergency resolution and voted to join the confederacy. The secession ordinance explicitly stated their purpose of doing so - their lawfully elected government and lawfully convened state militia was literally being attacked and overrun by the federal army!
Similar abuses by Lincoln reached into the highest levels of the government. On the outset of the war, he had a U.S. Congressman from Maryland arrested and imprisoned. A few years later federal troops arrested and deported the leader of Lincoln's critics in Congress, former Rep. Clement Vallandigham of Ohio. In May of 1861 Lincoln even ignored a Federal Court ruling by Chief Justice Roger B. Taney overturning his order to suspend habeas corpus. In any other time, this would have been an impeachable offense. And that goes without mentioning that some evidence exists that Lincoln or others in his administration were even considering, at one time, arresting Taney himself over the ruling.
Now, if none of that is a disruption of the way our Government operates and operated, I do not know what is!
Also, no contingency of war prevented Jefferson Davis from appointing federal judges, etc.
Actually, one did indeed exist. It was called the Confederate Senate and it actively sought to halt judicial appointments out of fear that they would be used to assert national control over the state militias, which many governors wanted to control themselves.
The issue of whether or not the president may suspend the Writ has never been decided.
"Lincoln, with his usual incisiveness, put his finger on the debate that inevitably surrounds issues of civil liberties in wartime. If the country itself is in mortal danger, must we enforce every provision safeguarding individual liberties even though to do so will endanger the very government which is created by the Constitution? The question of whether only Congress may suspend it has never been authoritatively answered to this day, but the Lincoln administration proceeded to arrest and detain persons suspected of disloyal activities, including the mayor of Baltimore and the chief of police."
-- Chief Justice William Rehnquist, Noevember, 1999
But Mr. Lincoln can speak for himself
"After the battle of New Orleans, and while the fact that the treaty of peace had been concluded, was well known in the city, but before official knowledge had arrived, Gen. Jackson still maintained martial or military law. Now, that it could be said the war was over, the clamor against martial law,, which had existed from the first, grew more furious. Among other things, a Mr. Louiallier published a denunciatory newspaper article. Gen. Jackson arrested him. A lawyer by the name of Morel procured the United States Judge Hall to issue a writ of hebeus corpus to release Loualier. Gen. Jackson arreted both the lawyer and the judge. A Mr. Holander ventured to say of some part of the mater that "it was a dirty trick." Gen. Jackson arrested him. When the officer undertook to serve the writ Gen. Jackson took it from him, and sent him away with a copy. Holding the judge in custody for a few days, the general sent him beyond the limits of his encampment, and set him at liberty with an order to remain till the ratification of peace should regularly be announced, or until the British should have left the coast. A day or two elapsed, the ratification of a treaty of peace was regularly announced and the judge and the others were fully liberated. A few days more and the judge called Gen. Jackson into court and fined him $1,000. The general paid the fine, and there the matter rested for nearly thirty years, when Congress refunded principal and interest. The late Senator Douglas then in the House of Representatives, took a leading part in the debates, in which the constitutional question was much discussed. I am not prepared to say whom the journals would show to have voted for the measure.
It may be remarked: First, that we had the same Constitution then as now; secondly, that we then had a case of invasion, and now a case of rebellion; and thirdly, that the permanenet right of of the people to Public Discussion, the liberty of speech and the Press, the trial by jury, the law of evidence, and the Habeus Corpus, suffered no detriment whatever by that conduct of Gen. Jackson, or its subsequent approval by the American Congress."
Jackson wasn't even the president.
It's simply beyond you to be fair, isn't it?
Walt
The governor at least was a secessionist and traitor.
Walt
What a crock of crap! Missouri was split, like the other border states, on the question of secession. While it is true that the state convention voted unanimously not to secede in March 1862, the arsenals that you speak of were federal arsenals and Governor Jackson had no legal right to seize them. So the sending of militia to seize it was illegal. You say that 'feds responded by marching the U.S. army on the state capital to oust the governor and state legislature' which is nonsense, and that 'the state government convened in October in the town of Neosho' which is false. The legislature remained in office, and Claiborne Jackson was impeached and removed from office. It was the impeached governor and the minority of the state senate which met in Neosho and voted secession, something that they lacked the authority to do. So Missouri remained legally in the Union throughout the war, and while she did send men to fight on both sides the majority fought for the Union.