The choice of phrase is important, “separation of church and state”. Jefferson doesn’t say separation of religion and state. He is talking about institutionalseparation. Ireland’s official church is the Roman Catholic Church, as is Poland’s. In England, it’s the Church of England. These aren’t religions in general but specific religious institutions. No nation has “Christianity” as the official state religion for a very good reason. The reason is that there’s about 50,000-some odd flavors that run the gamut from the Mormons to the Unitarians. Some Christians say Jesus established a hierarchical church, others say he was a social activist, still others say he was an anarchist. Saying Christianity is the official state religion would border on effective meaninglessness. It wasn’t the ideas that the Founders were afraid of which is why they were perfectly free praying together and expressing religious sentiment in public documents and speeches. Institutional corruption and tyranny were their concerns.
The results of institutional mingling of churches and governments are quite clear in history and it hasn’t been beneficial for the state or the church. However, this is a far cry from divining an intent that projects the idea that “religion is all that’s wrong with the world” upon the Founders. There was a camp among the Founders who believed that a free society required a religious people and yet still continued to allow free association between the various churches.
However, the crowd pushing separation most vigorously also is the crowd that’s trying to regulate certain religious beliefs out of existence. Pharmacists aren’t allowed to express their religious sentiments about abortion and retain their jobs. The argument is that they shouldn’t take the job if they don’t follow a pre-defined ethical construct approved by the government. Catholic hospitals are consistently fighting attempts to force them to provide abortions despite their clear religious teaching. Catholic Charities in California are required to recognize “gay marriage” despite their own beliefs. Schoolchildren (a.k.a. individual citizens not to be confused with government officials) are told that they aren’t allowed to pray or have Bible studies on school property. In one case, school children were threatened with federal prison if they dared utter a prayer on their own volition during a graduation ceremony. The IRS has investigated churches for preaching against abortion. In short, the wall of separation is growing to enforce a certain religious orthodoxy and not protect the free expression of religion that was also mentioned in the First Amendment.