The separation of Church and state?

Just because there is one main/original reason for something does not mean that there is only one purpose for it. This is equivalent to arguing that because the internet was originally founded for governmental reasons that the secondary purposes to the internet such as emails, research, youtube videos, and others are useless. Just because the separation of church and state was originally there just to protect religion from the state does not mean that it cannot be applied to protecting the state from the church.