You need to talk to your kids directly.

"Sparky and Dougie, grandma is sharing her ideas but many people feel differently. Mom and I do religion differently. We love grandma but we don't agree with these ideas. In our family we believe / don't believe X and Y."

It's up to you to bring your kids up in the belief / non-belief of your choice.

If your MIL undermines it, at least your kids will know that this is one opinion among many -- which sounds like your and your wife's religious philosophy.

This is the cost you pay for saving on childcare.