Currently watching "She Wore a Yellow Ribbon" (John Wayne/John Ford) and the movie, set in 1876, has made references to several former Confederate soldiers serving in the US cavalry, including one former Brigadier General who now serves as a lowly trooper who passes away, being buried with a makeshift Confederate flag that the Union provides! Was this actually common, or a typical Hollywood historical error? The men also seem to not mind serving with former Confederates, even John Wayne's character, a veteran of Sherman's army. Would this also be typical?
I have not seen the exact movie you are talking about but there are some instances of former Confederates becoming members of the U.S. military during/after the war. Joseph Wheeler was a key calvary commander for the Army of Tennessee during the Civil War and later become a Major Genral of Volunteers during the Spanish-American War (although he was also a congressman In the interim so he was certainly reconstructed to a certain extant).
http://en.m.wikipedia.org/wiki/Joseph_Wheeler
Also there are Confederate POW's who fought under Geneal Pope in Minnesota during the Civil War against the Plains Indians. This was done to free up troops to fight on the main fronts and was successful to the best extant of my knowledge.
http://www.archives.gov/publications/prologue/2005/winter/galvanized.html
I don't know if that answers all your questions but the two examples came to mind.