What is the correct balance between protecting the freedom of religion, maintaining the separation of church and state, and protecting people from discrimination?

The past conflicts on religion have taught modern-day governments that all people have the right to practice their faith.  However, affairs of the state should not be influenced by any institution religious or otherwise.  As we have seen in the past when faith and politics mix, it always leads to conflict as the church has a tendency to prioritizes its policies above all else.  A good of proof of separation of church and state is when government allows religious minorities to practice their faith without fear of discrimination from the religious majority.