I have had similar worries to op. This is how it went:
My DD goes to a community primary.
We are atheist/humanist at home. DH is intolerant of religion. I am not a fan and don't believe in God, but I won't insult a believer for their faith. They can live on their cloud and I will live on mine, so to speak.
My daughter, probably because of our influence, doesn't believe in God, or what the bible says, or indeed any religious script. She does have an interest in paganism, so spirits rooted in nature, and we let her get on with that (she has the Green Man on her wall, stone fairies around her room, and a wand blessed by a white witch. You get the idea).
My DD has been taught about different religions since year 1 whilst doing the Christmas play each year. She once had an RE teacher visit who insisted the children treat the bible as truth, like a handbook. She said she told this teacher that it was a storybook that made no sense in plot (she is also a budding writer) which shocked the teacher. I was called in, and I had to explain that DD wasn't being insulting but that she just regards the Bible as a story and not much else.
Once her good friend who wears a headscarf was being bullied and said headscarf was pulled off her head. DD got right in there, pushed the bully over, and retrieved the headscarf. The teachers pulled her to the deputy head's office and he asked what went on. "Kay was being bullied and her headscarf was taken and she is my friend so I had to get it back because it's her religion and culture," she replied. She was let off, and the bully got detention. So she knows that modesty is asked for from some believers.
She has Catholic, Muslim and Hindu friends. She likes going to her Muslim friend's house for tea because the food is "epic". Her Malay friend likes coming to us because she gets to eat Toad in the Hole or Shepherd's Pie. She get Malaysian food at home all the time.
The law still says that schools should have assemblies that are essentially Christian in nature but I know that if our school did that, most of the kids would fidget and giggle, so they are now more along ethical or philosophical lines.
My point is, really, is to chill out. I was a flag waving, fist punching, militant atheist at one point and thought sending my daughter to a community primary would keep her away from those Christian zealots. In fact, she has had a well rounded Religious education and her cultural experiences have been fantastic.
Finally, we don't celebrate Easter, at all, really. But DD is up for saying hello to the Goddess of Rebirth, Eostre. We are going to have Eostre eggs and plant some stuff in her honour. We can go along with that.