I had a similar experience with a lady who wanted very much to join the local chapter of the Daughters of the Confederacy. As evidence she produced a discharge for her ancestor dated August 1865. It also had an eagle emblazoned at the top of the document, a bad sign.

Turns out that he switched to the wrong side before the war ended. I suggested she try another ancestor.

People assume that ancestors made this choice for political reasons. Many were influenced by the Federal government's ability to provide pay for their services and provisions for their families, something Confederates never had regularly if at all. Brand new arms and equipment and uniforms also made a favorable impression.

Finally, the great majority of Southerners who enrolled in Federal service did so during the last two years of the war, after it was clear to most which side would win.