There's another very different version on the Red Clay Rambler's Hard Times album. The story in it has degenerated considerably - no motive for the murder is mentioned, for instance. The lyrics go like this:

Two lovin' sisters went a-walkin side by side
Oh, the wind and rain.
The one throwed the other in the water so wide,
And she cried the dreadful wind and rain.

She floated on down to the miller's millpond
Oh, the...
Yes, she floated on down...
And she cried...

The miller fished her out with his long hook and line...

He made fiddle strings of her long curly hair...

He made fiddle screws of her little finger bones...

But the only tune that fiddle would play was
Oh the wind and rain
Yes the only tune that fiddle would play was
Oh the dreadful wind and rain.

The tune's completely different too but it's interesting the verse structure is the same (line, refrain, line, refrain).