Ok - look at the verse under discussion.

'I danced on the Sabbath and I cured the lame
The holy people said it was a shame
They whipped and they stripped me and they hung me on high
And left me there on a cross to die'

Maybe it is a little misleading but, in order to make it scan, how could SC have phrased it? Try putting in 'The Romans' - it won't scan.

Occasionally a songwriter might have to play with the accepted story in order to make a song that satisfies. I would warrant that very few people, unless, as Al says, they are looking for insult and slight, would take Carter's words as being anti-semitic.