We had similar suggestions. I actually quite liked the idea that people might take something to eat, and then find a lot of others had done the same.
The water into wine was funny, raising Lazarus from the dead was another story for discussion.

I don't see why a religious education class couldn't encourage children to question the bible, or any other religious teaching. We never had the multi faith education they get now...odd that I have never felt the need to attack anyone because of their belief system that I know little about. My son went to school and was shocked to find he had to pray. The concept was unknown to him. He had never heard of God or Jesus or even church. Never occurred to me, living the way we did. The subject just never arose.

We were told that the bible should not be taken as Gospel ☺️ . It was written so long ago, often transcribed stories that had been passed down orally for perhaps many years by superstitious people who sought to explain the often inexplicable, and then translated several times, by people who might be guessing at some of the words, and who would be influenced by their own beliefs.
We didn't have a religious teacher. I think the headmaster just felt someone should turn up now and again, as in general we treated it as a free period. Many of us envied the RC pair, who, when he did deign to visit, were excused and really did have a free period.