Briefly, separation of church and state extremists are required to turn a blind eye to history, or to view history with the eye of bigotry, in order to maintain their extremist position. They tell us that the Constitutional framers wanted to divorce religion completely from government, ignoring the fact that the same people who considered and passed this amendment hired chaplains, held Congressional prayers, etc. In other words, to maintain the position that the framers wanted to divorce religion completely from government, one must also believe that they violated the very law that they themselves had passed.
Now, one can try to make the argument that they passed the amendment and then forgot about it, and violated it. But this is rather foolish considering the fact that they themselves had considered the language of the amendment, discussed, and voted on it within the very same time frame that they committed these "violations."
Further, one can try to make the argument that they willfully violated the amendment, knowing very well that they were intentionally breaking a law which they had just passed. But this requires us to call them guilty until proven innocent.
Much more likely, and reasonable, is the notion that they didn't pass the First Amendment to support a separation of church and state extremist agenda. They passed it instead to prevent the establishment of a national Christian denomination within the United States. They had only to look to the history of Europe to note the severe problems that arise when a nation adopts a particular Christian denomination as an official state religion. Whether we consider the Thirty Years' War, the Elizabethan conflict with the Catholics, the French massacre of the Huguenots, or other examples of European persecution of Christian minorities, we see very clearly the problems that the establishment of religion brings with it. The framers intended to keep this country from such problems, and did so successfully.
Now, let's take a look at some of the problems with the extremists' interpretation of the First Amendment:
The first Congress held Congressional prayers.
The first Congress asked the President to declare a day of thanksgiving.
Supreme Court invocation.