A point that's just occurred to me is that LOTD isn't actually telling the story of Christ's life and death. It's so abbreviated that without prior knowledge of that story it is all but meaningless. Both the singers and target audience are almost certainly aware of that story, and the song simply cues references to different parts of it. So the first part of the contentious verse refers to one incident, and the second part to an entirely separate, later incident. Anyone listening to the song with that background knowledge would realise that and would not make the connection that Gerry is claiming, unless they were determined to find the most tenuous excuse for anti-semitism, which Gerry appears to be doing.

Also, I think it's possible to be anti-Jewish, in the sense of being critical of the actions of certain Jews, without being anti-semitic, which means hatred of all Jews. Even then, the verse in question is only critical of the hypocrisy in the first part - the second part simply references the events (whether or not you accept their historical accuracy) without comment.