Based on the evidence (or lack of it), it's much more likely that this man died before the war began. First, older men with families ordinarily didn't leave families to fend for themselves at home. Volunteers were usually younger, single men like the Winfield Scott of Ponotoc County that you mentioned. According to the census, Winfield Scott would have been seventeen in 1860.

Aside from not being able to find Winfrey Scott, I can't locate children such as Gillum Scott, who should be fifteen by 1860. Polly Scott disappears as well. Perhaps she died or remarried by 1860. If the latter, the Scott children may be reported on the census under her new husband's name. My wife's ancestor named Gray is reported on the 1870 census under his step-father's name, Dennis. This cannot be an isolated incidence. He reappears on the 1880 census as an adult using his actual name, Walter M. Gray.

Another man named Winfrey Bond Scott served in a Louisiana regiment during the war. Please don't get him confused with your Winfrey Scott.