The Hacker article cited by the NYT is worth the time reading and considering.

Considering the currently accepted number of Confederate wartime deaths, read this by Michael Lind. Conditions and facts conveyed in this statement have constantly been in my mind since reading them seven years ago. They influence the way I respond to questions about the Civil War, particularly its outcome and impact on those who survived in the South, black and white. If my posts include unpleasant words from time to time, I apologize in advance. The underlying reason usually has something to do with the paragraph below.

The South had been ruined by the Civil War. Two hundred and fifty thousand Confederates died of wounds from battle or disease. If the Union had suffered proportional losses, instead of losing 360,000 men, they would have lost more than a million. The equivalent to the South's losses by the United States in World War II, in which the nation lost more than 300,000, would have been more than 6 million.

In addition to conquest and occupation, Southerners experienced losses on a scale suffered by European nations in the world wars of the twentieth century. The abolition of slavery erased $2 billion of capitol. Two-thirds of southern wealth vanished. Between 1860 and 1870 the South's share of U.S. wealth shrank from 30 percent to 12 percent. By 1880 the gap in per capita wealth between the North and South was comparable to that between Germany and Russia.

Michael Lind, What Lincoln Believed: The Values and Convictions of America's Greatest President, p. 240. I will be pleased to share Mr Lind's sources for the statements given here.

The Alabama State census of 1866 includes three columns for each head of household. These record the number of household members killed, died and disabled during the war. I don't know of any state or county totals compiled, but surely these exist.

This side of heaven, there's no reasonable way to calculate the number of post-war deaths due to wartime wounds, disease and/or exhaustion.