The separation of church and state minimises the tendencies of a group that claim to be morally unquestionable, and use this claim to persecute minorities (and/or non-believers) and assume authoritarian rule. We need the morals and methods of any governing party to be questioned at all times. Saying something is gods will or inherently just is unhelpful to discussion and derails meaningful narrative.
Countries that have very close ties between church and state often carry out religious persecution on minority cultures. One example of this is Iran were the country is run by Supreme Leader Ayatollah Khamenei, acting as both head of state and highest religious authority in the country. In Iran, the largest religious minority is that of the Bahá'ís who are not only marginalised but subject to violent attacks, imprisonment, torture, and a monumental propaganda campaign by state sponsored media.