The way I see it:
I'm going to start off by saying that a society like the USSR did not so much 'kick religion to the curb' so much as decide to start an atheist theocracy. Which, makes sense. No totalitarian state is going to want to share power with any church. As such, the USSR is actually very antithetical to separation of church and state.
Anyways, back to how I think separation of church and state should be handled:
1. The Church is not God. A Christian preacher's job is to recruit more Christians, for God's sake. A Christian plumber's job is to fix people's pipes, for God's sake. Neither job is more holy.
2. Do not let the government control the church. Otherwise, they'll twist the church into propaganda tool for any political agenda they like.
3. Do not allow the church control the government. Otherwise, they'll become obsessed with political power rather than spiritual enlightenment.
4. Yes, the government should work for God, in a sense. No organization should try to wholly separate itself from God. Especially not Government. God is the ultimate statesman, and has jurisdiction that transcends our plane of existence.
The intended result of these principles are this:
The state must be founded on concepts such as natural laws and God-given rights. Exactly what this means is up for debate, but they are principles that should be in any law maker or voter's minds. For similar reasons, nobody should refuse to turn something into law because it has religious inspiration. That the bible says "Do not murder" does not mean that murder should be legal. Also, it's fine for government officials to do things like have "In God we trust" written on coinage. However, this has to apply equally to all religions. There can be no law forbidding muslims from posting "In Allah we trust" on coinage, either, if they can get enough support.
However, the other caveat is that government should not try to take over church duties. For example, the government cannot do things like outlaw pornography or gay marriage. It's the job of the church to render them a non-issue through nonviolent means.