It's awkward because many Christians see the 'seperation of Church and State' as being a discrimination against them, especially when it can be end-run by saying you are an Atheist, and therefore there is no Church to seperate. So an atheist can say "It is my moral, non-religion belief that X should be banned", and there's still seperation, but a Christian stating the same view as a Religious belief hits a brick wall. In that respect, it's makes a tricky road to walk.
When I go to Church for weddings etc, I don't make a scene, I just sit silent during the Lord's prayer, or occasionally mumble "We are the Borg, your technological and biological distinctiveness will be added to our own. From this point onwards you exist to service....us. Resistance is futile. Amen", but only if I had a bad day.
I also see the Atheists point of view, that it is a creeping situation, where prayers for a specific belief system are being slotted into multi-cultural systems and that is wrong. On balance, I think it's more the small-mindedness of the people involved, rather than religion itself that is to blame here.