Back in Lincoln’s time, we didn’t have civil service laws. A very large percentage of government employees are Democrat, would refuse any martial law attempts by Trump, and the judges would back them.
Judges have no power to enforce their rulings. The President is Commander-in-Chief and as such commands our military. I.e., there is nothing a judge can do if a President chooses to ignore a court ruling, which conflicts with the President's executive order to suspend habeas corpus. The President is not a lesser branch of government.
Excerpt from thoughtco.com:
"In response to the arrest of Maryland secessionist John Merryman by Union troops, then Chief Justice of the Supreme Court Roger B. Taney defied Lincoln 's order and issued a writ of habeas corpus demanding that the U.S. Military bring Merryman before the Supreme Court. When Lincoln and the military refused to honor the writ, Chief Justice Taney in Ex-parte MERRYMAN declared Lincoln's suspension of habeas corpus unconstitutional. Lincoln and the military ignored Taney's ruling. On Sept. 24, 1862, President Lincoln issued a proclamation suspending the right to writs of habeas corpus nationwide. "Now, therefore, be it ordered, first, that during the existing insurrection and as a necessary measure for suppressing the same, all Rebels and Insurgents, their aiders and abettors within the United States, and all persons discouraging volunteer enlistments, resisting militia drafts, or guilty of any disloyal practice, affording aid and comfort to Rebels against the authority of United States, shall be subject to martial law and liable to trial and punishment by Courts Martial or Military Commission:" Additionally, Lincoln's proclamation specified whose rights of habeas corpus would be suspended: "Second. That the Writ of Habeas Corpus is suspended in respect to all persons arrested, or who are now, or hereafter during the rebellion shall be, imprisoned in any fort, camp, arsenal, military prison, or other place of confinement by any military authority of by the sentence of any Court Martial or Military Commission." In 1866, after the end of the Civil War, the Supreme Court officially restored habeas corpus throughout the nation and declared military trials illegal in areas where civilian courts were again able to function.
On Oct. 17, 2006, President Bush suspended the constitutionally bestowed right of writs of habeas corpus. President Abraham Lincoln did the same thing 144 years ago. Both presidents based their action on the dangers of war, and both presidents faced sharp criticism for carrying out what many believed to be an attack on the Constitution."