Firstly, this is a song - song lyrics usually have to fit into a tight rhythmic structure as well as conveying meaning in an effective and memorable way. This can result in some loss of subtlety, or in phrasing which may be capabable of different interpretations.

Secondly, it was written as a song affirming Christ and as a metaphor for his life, death and resurrection. The lines about the "scribes and pharisees" seem to me to reflect that Jesus, a Jew, took his teachings to the Jewish people and was rejected, especially by the Jewish establishment of that time. The same goes for the lines about curing the lame on the sabbath and the "holy people said it was a shame" - the (Jewish) religious authorities disapproved of his activities.

I am neither Christian nor Jewish, so can someone please explain why it is anti-semitic to say that? It seems to me to be a very long step from words which tell, in a necessarily simplified form, the story of Christ to the anti-semitic meaning which some are seeking to read into them.

As for the song making me cringe, that's another matter, but I struggle to find anything in it that makes me think it's an attack on the Jews.