It's more likely for civilians in central Alabama to be struck by lightning. However, it did happen. While speaking with two Confederate soldiers, David Hanby was shot and killed on April 18, 1865. This incident in described in the History section of an article on Turkey Creek --
http://www.bsc.edu/sec/ecoscape/turkeycreek.cfm

Frequent moves by families in the South are well documented. Comparison of the census in an Alabama county from one decade to the next will demonstrate remarkably high turnover, old residents leaving and new families taking their places. The Civil War displaced untold numbers of people in the South. If you cannot locate family members on the 1870 census who were recorded ten years earlier, death, dispersion and remarriage could explain their disappearance.

Here are two examples.

At the time of the Civil War my ancestor James Madison Shelby lived along the Perry-Bibb County line in the community of Jericho. In 1869 a family group consisting of himself, his wife, a son and six daughters plus a number of in-laws left Alabama for Texas in three wagons. The only family member remaining in Alabama was my ancestor, James Adams Shelby, who had recently married and started a family. Along with the death of a daughter in 1862, this accounts for at least a dozen Alabama residents not found on the 1870 census of that state.
http://freepages.genealogy.rootsweb.ancestry.com/~beckenbachsimons/jamesmadisonshelby.htm

In my wife's family, remarriage accounts for a family's disappearance. In 1860 her ancestor Pleasant Gray lived in Shelby County (named for Isaac Shelby, a distant relative of J M Shelby) with his wife and three children. "Pleas" Gray died of wounds in Virginia during the war, and his wife Sarah Crosby Gray remarried in 1867. In 1870 family members (the former widow and her three children) are recorded under the new husband's name, Dennis. If you didn't know that Sarah Crosby remarried after Pleasant Gray died, she and her children just seem to have disappeared.

I hope this helps. of all the reasons for someone to disappear, death due to combat in central Alabama would be at the bottom of the barrel.