I contemplate with sovereign 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 & State.(http://www.loc.gov/loc/lcib/9806/danpre.html)That interpretation, which is also reflected in correspondence among other principals at the time, has been upheld by the courts consistently. It was never intended as a rejection of religion. Rather it reflected the belief, common at the time, that religion was a personal matter and not the stuff of government. That there were variations in attitude among the state governments was itself one of the reasons why the states did not want the federal government involved.
In fact, none of the rights stipulated in the Bill of Rights, including our own favorite second amendment, applied to state governments at all. Only with the adoption of the 14th amendment did state governments fall under the constraints of some of the first ten amendments, including the first, but not the second. The first time in history that the Supreme Court ruled that the second amendment applied to the states by virtue of the equal protection clause of the 14th amendment was this year.
So yes, the Constitution was intended to build a wall of separation between church and state by virtue of the first amendment. It has been interpreted that way throughout our history. It has only applied to state governments since the civil war. The only modern "revisionism" affecting the Bill of Rights has been in extending the application of the second amendment to the states.