I think it's best to cut out proxy measures whenever possible. For instance, if we want our policies around charities to maximize societal good, then we should base charitable status on societal good directly instead of basing it on religiosity, assuming that religiosity translates into societal good.You're quite right. And I wish that we didn't. Governments validating "religion" merely serves to enshrine particular notions of what religion is, thus it hardly serves all religions equally, much less irreligion.
This works - and improves things - even if we assume that religiosity does translate into societal good the vast majority of the time.
... but since I don't think that preferential treatment of religion is going away any time soon, we're going to have to keep on deciding which religions are valid and which aren't... every time someone asks to wear their hijab, turban, or colander for their driver's license photo.