You've got the date wrong. The Supreme Court has relied on the Danbury Baptist letter since 1878, less than 90 years after the First Amendment passed. It has been the interpretation for 134 years now.
During the 1870's, the US Supreme Court, the ultimate arbiter of the Constitution, utilized the phrase "separation of church and state" in the case of Reynolds v. United States (1878). In Reynolds, the Supreme Court upheld the application of a federal law, making bigamy a crime in the territories, to a Mormon claiming polygamy was his religious duty.http://www.ifas.org/fw/0003/wrong.htmlThe Court's opinion stated: " I contemplate with .reverence that act of the whole American people which declared that their legislature should 'make no law respecting an establishment of religion or prohibiting the free exercise thereof, 'thus building a wall of separation between church and state." The Court further stated that Jefferson's term 'wall of separation between church and state' may be accepted almost as an authoritative declaration of the scope and effect of the [First] Amendment."
I would also note that nowhere in the Constituion is teh Supreme Court called teh final arbirter of the Consitution. In fact, Congress has the explicit right to take issues out of the range of the USSC.