I have a bias against religion. I'm tired of the zealots. For instance, I'd vote for an atheist if I thought they were qualified. I'm ok with gay marriage.
But I'll listen to your terms!
I'm a Christian, and when it comes to politics, religion isn't a decisive factor. I could vote for an atheist who takes the right positions, is trustworthy, etc. A large number of the political thinkers and commentators I respect are not Christians. I'm not sure how many of them are atheists, but plenty of them are Jews (both secular and orthodox).
Nevertheless, having a bias against something may impact how you vote, but it isn't supposed to impact how you would rule on a judicial matter. For example, I have much more than a bias against flag burning. I detest it to no end. However, as a judge, I'd never allow a federal prohibition on flag burning to stand. The point is that a judge has to be able to set aside his or her biases (which we all have) and apply the law as it was intended by those who adopted it.
As for the establishment clause, there's no indication that a complete separation of church or religion and state was intended. For starters, the First Amendment's language simply isn't that broad. It prohibits Congress from making a law "respecting the establishment of religion." If they had intended something broader, they could have used such language.
Second, the historical context of the First Amendment doesn't support that broad of an interpretation. They were trying to avoid the merger of church and government that existed in England and didn't want the government persecuting religious minorities. They didn't want an official religion and definitely didn't want the church to be directly in the sack with government, as the Church of England was. They considered that bad for both government and the church.
However, there's no indication that the founding fathers had some sort of inherent contempt for religion or its influence on culture or even politics or policy. Bear in mind that they didn't even restrict state governments' establishing religion. To them, if a state wanted to have an official religion or even a taxpayer-funded church, they were OK with that.