Let's see...
After the Civil War, the Radical Republicans gain full control of the US government upon Lincoln's death, institute draconian military rule of the southern states, including permanent disenfranchisement of anyone who fought against the Union, and institute radical abolitionist and racial equality policies. This is done in philosophical alliance with certain New England abolotionistprotestant church groups (Congregationalists, northern Baptists, and others) which ultimately gain considerable control over the ideals and programs of the Republican party on other issues as well (temperence, etc,). Churches which remained lukewarm or divided over abolition are subjected to unofficial discrimination. The North becomes very puritan. THe US Govt also uses Christian missionary activity among southern blacks as the main tool for educating and uplifting them
Meanwhile in the south, white resentment and hostility to the more dictatorial northern occupation and long term black/carpetbagger rule is worse than in OTL, but is driven completely underground by harsh repressive measures. White southerers turn to racialistic, semi-fascist political philosophies, which blame, among other things, the northern churches for their loss of power. The strong evangelical Chistianity of blacks, mission work by northern churches in black communities, and inclusive teachings of Christ only reinforces this view, which makes all Christians suspect. Finally, during the early 20th century, the southern whites finally regain political local auhtority, although in a context when minority black rights are still strictly protected by (the more intrusive) Federal govt. Majority white dominated state governments use there new political authority to strictly limit the role of religion in public life, including banning all government sanctioned expressoins of religion.