1) Atheism is not a religion.
B) The removal of God from government actually increases freedom because not everyone believes in the same God or Gods. Some don't believe in God at all. What if it were decided that all references to God should be changed to Allah? All of you would be up in arms about that. Don't impose your God on others and set an example for how a government should be run instead of fighting theocracy with theocracy of a different flavor.
Not necessarily it weakens by breaking down your faith (their hopes anyway), not everyone looks or talks alike either so should that be changed as well? If this nation was founded under allah then it would not matter, but it wasnt and by an athist or any other religion/group imposing their wishes by getting it removed/taken down or what have you ... how is that any different?