Booth's successful attempt wasn't the first attempt against Lincoln. Nor was Jefferson Davis immune to such actions as he also was a target, i think, of a couple of attempts. Just because the Army of Northern Virginia had surrendered did not meant that all of the other Confederate armies, or that the Confederacy itself, had quit fighting. Although the die may have been cast, the last Confederate army did not surrender until 7 weeks later in the Trans-Mississippi.
By the time that the Army of the Potomac had reached Petersburg in 1864, 90% of its command structure from Lieutenant's to Major General's had been killed or wounded in just the two months from May 1st to July 1st, 1864. Certain Brig. General such as the first Union Brigade to enter the Crates, would not even lead their men, but remain far in the rear in a bunker because of this.
Taking out the enemy high command structure is, and always has been, a legitimate function of War, even today. Are we not targeting the leaders of Al-Quida with our Drones? What is the difference between a .41 caliber derringer bullett and a 1,000 pound JDAM? Should we now stop hunting for and targeting Osama Bin Laden for elimination because he is the head of the radical Muslin element that has sworen war against us?
NOW, I will say that unlike Lincoln, the assassinations of Garfield, Kennedy and the other Presidents in our history, and the attempted assassination of Ragen were "political assassinations" as they were not engaged in a war against the people who attempted those assassinations.