When government and religion are intertwined, there are almost always issues. Look at when Christians had control of the world. We had the crusades, people being hung for stealing loaves of bread, and the Inquisition. And now, the Islamic countries have some of the poorest quality of life on the planet.
We are not at the endtimes and we do not appear to be nearing the endtimes (at least I certainly hope not), so there is no reason for religion to take a place in modern government, where we have carefully placed the basic morals of living in society into a legal context without the complications of religion.
The last thing we need anywhere in the world is a combination of church and state. That's what the Taliban are/were. Here in the United States, we have a number of extremist religious bigots who are trying to rewrite the Constitution to make this a Christian theocracy. That would be a disaster if it happened.
Yes, separation of church and state is best for democracy. Historically, organized religions and/or "the church," have been rather controlling when they were able to be because they were in power in government. Religious views can be disruptive to regular political processes and therefore they should be left out of government.