Before the War Between the States, the South was much more ethnically and religiously diverse than the North. While anti-Catholic Know-Nothing mobs were busy burning down convents and churches in Philadelphia and Boston, the South was 25% Catholic and the largest synagogue in the US was located in Charleston, SC and held that record until a larger one was built in Brooklyn in the 1890's. Pope Pius IX was the second head of state to recognize the Confederacy (after the King of Siam). Most of the Jewish slave traders operated out of the North, not the South.
It was Yankee carpetbaggers, robber barons, and politicians in league with certain opportunistic local landowners and businessmen, who introduced anti-Catholic bigotry, Jim Crow laws, and persecution of the Jews into the South during so-called "Reconstruction." President Andrew Johnson wanted to end Reconstruction quickly because he knew the damage it was causing to the Southern way of life and the Southern people in general. The Yankee congressmen had other ideas. In the words of Representative Thaddeus Stevens of Pennsylvania, ex-member of the Know-Nothing Party and Radical Republican,
Reconstruction must revolutionize Southern institutions, habits, and manners ... The foundations of their institutions ... must be broken up and relaid, or all our blood and treasure have been spent in vain.
He also said: ...the adoption of the measures I advocated at the outset of the war, the arming of the negroes, the slaves of the rebels, is the only way left on earth in which these rebels can be exterminated. They will find that they must treat those States now outside of the Union as conquered provinces and settle them with new men, and drive the present rebels as exiles from this country....They have such determination, energy, and endurance, that nothing but actual extermination or exile or starvation will ever induce them to surrender to this Government.
Among those rebels he wanted to drive into exile were many good Catholics. What happened after the War, if it had occurred today, would be classified as "ethnic cleansing." Catholics were driven out of the South and the fundamentalist holy-roller Halleluyah sects replaced the more moderate Protestant denominations that most Southerners had belonged to before the War. Hooded "night riders" who attacked Catholics with as much vehemence as blacks terrorized the rural areas and small towns. And the South remained trapped in poverty for more than a hundred years.