There is no way to know if Henry Thomas wrote the tune or not (though I like his energetic version more that Old Crow's more laid back approach), but the melody obviously existed long before OCMS. I think the proper thing to do is to claim copyright on an arrangement w/ additional lyrics of a traditional tune. The reason for not doing so is simple: money. Royalties on arrangements are roughly half of what they are on fully copyrighted compositions. Perhaps someone outside the band made the decision to credit it the way they did, which, in my opinion, is ignoring the origin of the song. I have always appreciated The Rolling Stones for making sure that guys like Fred McDowell & Robert Wilkins received their fair share of royalties.

Don't think for a minute that the Stones gave them their "fair share" out of any graciousness on their part -- I don't know about McDowell, but Wilkins was still kickin' around in the sixties, so his copyrights were probably still active. I mean, all those delta/memphis blues boys ripped their stuff off from others, too. So just because Wilkins was getting his "fair share", it doesn't mean the poor ol' feller who picked cotton all day and played on his porch at night (and might himself have even ripped the song from someone else!) ever saw a dime...

As for Wilkins, I believe he was not credited for Prodigal Son on the Beggar's Banquet credits, & the Stones were quite gracious in seeing to it that he got paid.