The main difference between then and now was the official declaration of war. If this president could get Congress to officially declare war against all Islamic states, perhaps we could arrest these clowns.
There was no congressional declaration of war during the Civil War. War can only be declared against another nation and neither the United States, nor any other nation on earth, ever recognized the Confederates as a lawful nation.
It is very similar with the jihadists today. There were lots of "sympathizers" both in the US and around the world, most notably the French government whores and British Imperial and mercantile classes who hoped to see the US "Balkanized" in the 1860s to advance their financial and colonial interests.
Then as now, the idea of a strong America frightened tyrants everywhere.