Personally having spent a fair bit of time in the Middle East, I'm glad I studied RE at school as it gave me a head start. Okay, I was in the advantageous position of spending a lot of my childhood in that part of the world, and you get your anecdotal edification - however, having a bit of structured learning about different cultures (where religion is a major part of it) is in my opinion priceless.
Though our school moved away from collective worship and assemblies were either agnostic/non religious, or you could choose to go to a Jewish/Muslim/Christian/Other religion assembly to suit your beliefs. I liked that, it meant I was able to go to Christian assemblies and be with people that wanted to be there rather than lots of resentful kids.
You don't have to accept or believe or anything like that, but knowing about it shows a bit less ignorance, and perhaps, just perhaps, help remove a little prejudice.
But it seems it is easier to have contempt (which is rather aggressive way to be IMO) for these things rather than accept them and have a vague amount of understanding about it.
However this is not the point of the OP, the point of the OP is that the rector does not seem to be performing to the level/standard that the parent (OP) is expecting and wants to have their child excluded from assemblies - I think it is a perfectly fair request.