Stan, I don't claim to be a forensic scientist, but many Confederate POW's suffered from scurvy and I believe one of the lessor common side effects was eye problems. Scurvy was rare in 19th Century America, except in yankee prison camps. That was because the prisoners were often (especially at Camp Douglas) denied fruit and vegetables. They were in ample supply, but withheld nonetheless, year after year and in spite of changing prison commanders. Other medical problems from malnutrition are numerous and when a man did get sick, he lacked the ordinary amount of white blood cells to fight off infections and heal.
Your ancestor was malnourished for long periods of time and likely suffered permanant damage as a result. In my estimation, those men, even yankee prisoners of war, were heroes. One caveat is the yankee prisoners at Camp Ford outside Tyler, Texas were not heroes because that was a relatively comfortable place.