In the Danbury letter Jefferson used the phrase and it was quite clear there and elsewhere that he was not refering to the weak version you pretend to.
Wrong Holmes. You are the one lying here. He was writing to the Danbury Baptists, and thus using their term. It's like the term pro-life. Pretty much everyone knows the term pro-life means anti-abortion, right? Some may argue it means anti-death penalty, and some pro-lifers are anti-death penalty, but that's not what the term means. Most pro-lifers are not necessarily against the death penalty.
So 200 years from now, someone reading a letter written to Dr Dobson claiming the Constitution is fully in accordance with his concerns and is "pro-life" should not refer to whatever "pro-life" means 200 years from now, but what it means today, and today it means anti-abortion.
You are reading a modernist interpretation of the term separation of Church and State back into history, and you are wrong. I am sorry that you cannot come to grips with historical reality, but it's not my fault that you cannot. The term "separation of Church and State" stems straight out of Anabaptism, not the Enlightenment.