As a parallel, we got married before the big ‘licencing of wedding venues’ thing. So our choice was between the local registry office (ground floor of 70s tower block) or local church (good for photos). So we got married in church having told the vicar that I was an atheist and Mrs Higs holds some sort of wooly belief that if we’re all nice to each other, everything will turn out all right and surely there’s got to be more to the universe than this???
It didn’t trouble me in the slightest but then I wasn’t asked to state a belief in god as part of the service.
So thinking about it, I probably wouldn’t have kids christened as an atheist myself just to secure them a better school, simply because I don’t like lying. Although I do understand that people do some very odd things for the (perceived) benefit of their kids.