The motto of the CSA was 'Deo Vindice' and the idea of God's Providence protecting the south shows up a lot on diaries and letters, but did any Confederates decide that defeat was the result of divine judgment?
Short answer: no, not explicitly. There were a few high-ranking, distinguished Confederate generals that supported official U.S. policies during Reconstruction, and dutifully supported various presidential administrations. For example, Robert E. Lee urged former Confederates to make peace with the U.S. government, and was vocal in his recriminations of those who sought to continue hostilities (either directly through guerrilla warfare, or by more passive means). Likewise, James Longstreet urged reconciliation and even worked with Grant's presidential administration (which didn't make Longstreet very popular amongst Lost Cause-ers). Famed cavalryman John Mosby similarly threw himself into reunification efforts, and encouraged his former comrades to do the same.
Although each of these men doubtless had their own personal reasons to encourage and even speed along reconciliation, what comes across in each as a common factor is intelligence. These are just three examples, but one gets the sense reading about Lee, Longstreet, and Mosby that they understood that they could make more progress reintegrating into society by working with their old enemies than continuing to fight a war that was already lost. U.S. Grant had kind things to say about each man, and especially re: Mosby, and seemed willing to help them all out since they had done so much to bring attention to the importance of reconciliation. The fact that these men were high profile, and commanded the respect of thousands, meant a lot to Grant and other Republicans, who saw their change in attitude as a brave (and smart) development that could only help bring the country together, and make life easier on the former Confederates.
This seems to be the key: on both sides. North and south, those that pushed for reconciliation and support of Reconstruction seemed to do so because they earnestly thought it was the best thing for the veterans. Nobody was going to benefit from an extension of the Civil War on "cold" terms (a-la cold war), so an understanding of this seemed to drive them (rather than a spiritual imperative).
[Sources - Bruce Catton, 'A Stillness at Appomattox'; James McPherson, 'Battle Cry of Freedom'; Jay Winik, 'April, 1865']