Natsku I assume you're not in the UK - that system is similar to the one in (our part of) Germany, except that it wouldn't even occur to a Bavarian (theoretically state not religiously affiliated) Kindergarten to offer the "miss out" option.
My nearly 5 year old has mainly picked up from Kindergarten that "One of the Gods is dead because he wanted to be king and the other king killed him, but in a really mean way with nails not with a sword in a fair fight, which wasn't... fair" 
But seriously, DC3 is my 3rd kid going through this system, we reinforce at home that some people believe X and some Y and some Z and some just don't know but like the stories... Mummy and Daddy think its all just stories like Hansel and Gretel and Snow White, but some of the stories are quite good ones, and some are scary and some are sad, and some we can learn something from - that doesn't mean they really happened...
Going from my own background (religious parents actively involved in their church, being told not to question what I didn't understand whenever I wanted to - question... religious schools with shed loads of compulsory worship and religion taught as truth:
I'd say that a thoroughly religious schooling is a damn good way to raise a good atheist, as long as you live in a relatively free society :o
So I'd let her go.
Also the stories and cultural references are useful groundwork if she is to have any hope of understanding literature and history.