The interesting thing about this is that the flag wasn't flown over the South Carolina state house until 1961, ostensibly to mark the 100 year anniversary of the civil war. Also Georgia didn't incorporate the stars and bars as their state flag (getting rid of a design created by a confederate veteran) until 1958/1959. That just so happened to be in the fallout of Brown v Board when many Georgia politicians threatened to close the school system over desegregation.

A book you might be interested in is David Blight's Race and Reunion. He discusses how the "emancipationist view of the war lost out to the "reconciliationist" view of the war. According to him many Americans became more concerned with reuniting the country than by remembering the final cause of the war, freedom and equality for African-Americans. The common valor of men on both sides became the focus and topic of numerous civil war reunions and memorials. So that may be one reason why; the North was more concerned about knitting the country back together than anything else.