Yes, I have found this a particular difficult hurdle to get over, and I still stumble a bit.
We are pretty much agnostic and my son when to a CBC initially as I really liked the school.
So he got Mary, Jesus and Joseph pretty much all day - and they had a rosary and the entire bit (very very Roman Catholic especially in his class).
I am not a catholic in any sense of the word, and am rather opposed so some of their beliefs, but .......
I decided to let it go and "go with the flow" of the school - he got really upset when he heard that Jesus had been killed. My son was CRYING UPSET when he came home before Easter, and needed to be consoled.
I did not contradict the school's teaching but I did find it was a great springboard to discussions.
I would keep asking my son "so what do you think?" or "what do you think really happened there...?"
My son after listening to a discussion about creation, asked me on the drive home how it was that there were dinosaur bones older than people were meant to have been around for, and how did God do it in 7 days. (I am simplifying what he said but that was the point)
I asked him again "so what do you think happened?"
And he came up with his own theory which I felt was a healthy mix of creationism and evolution.
I am sort of on the fence about it, so we discuss both ideas easily in our household.
My mother is a Jehovah's Witness so when my kids go there she chats to them and does bible stories and my kids refer to God as Jehovah.
My mom does not do Xmas or Easter, and chats to my kids as to why it is not part of her belief structure.
However I also discuss with my kids as to why we celebrate certain things and what it means to us as a family, and that we also respect others who might not share our belief system.
Our slogan is: "It is not wrong or right, or better or worse, it is just different..."
I also chat to them about other religions.
To be honest - for me it is important that they are exposed and they are tolerant.
It is so easy for us to push our ideas on our children and they believe only what we believe because that is what we were taught.
My theory is that my kids can negotiate their belief system as they get older, I merely act as a guide - and in some cases I honestly say "I don't know" when faced with something I am unsure of.
My kids go through "religious" stages.
My daughter likes a bible story at bedtime (she knew who Enoch was before I read the story, so I was mighty impressed), my son likes to pray at meal times .... my daughter loves to quote bible scripture at the most inoptune times ........we do neither as habit, but if they wish to do them, I am happy to walk the road with them.
We are not a religious family, but my kids are religious, and I am happy to sit and have healthy discussions about them on religion.
Some times it is hard as I am not always sure what I believe, so sometimes my head does hurt a bit following one of those discussions.
I am not sure if that "model" would work for you.