"All of those names are so common, as is John, that it's hard to use them as evidence, though." - Nicole
Yeah, it isn't, of itself, very strong evidence.
However, "Maggie D," if that what Neal sings, has special meaning, given that "Margaret Dabney" is the wife of record of Henry Dabney of Copiah County, MS.
Also, "Mary Magdalene" and "Maggie D" occur very rarely in the "John Henry" tradition. You might think that this would argue against "Margaret" as the original name. However, the oral ballad tradition is, I believe, follow a law much like Gresham's, "bad money drives out good." The "'Gresham's' ballad law" would be something like "bad facts drive out good," meaning that incorrect facts tend to replace correct ones. Part of what happens is that facts from lots of cases, which are woven into good lines, spread themselves out over all of the ballads.
Anyhow, the implication is that rare occurrences may be more likely to be correct than common ones, once a ballad has been transmitted through oral tradition for a while.