Daniel L. Dreisbach, Professor of Justice, Law and Society at American University, has written a pretty good article for Imprimus Magazine entitled "Origins and Dangers of the 'Wall of Separation' Between Church and State." The article makes the case that the "Wall of Separation" between Church and State as penned by Jefferson and mutated by the Supreme Court as a metaphor for the Consitutional Establishment Clause language is flawed. Of course, this is nothing new since many books have been written on this subject, including Robert L. Cord's book, The Separation of Church and State, which did an excellent job of analyzing the flaw in this approach nearly 30 years ago.
In his article, Prof. Dreisbach writes:
First, Jefferson’s trope emphasizes separation between church and state?unlike the First Amendment, which speaks in terms of the non-establishment and free exercise of religion. (Although these terms are often conflated today, in the lexicon of 1802, the expansive concept of "separation" was distinct from the narrow institutional concept of "non-establishment.") Jefferson’s Baptist correspondents, who agitated for disestablishment but not for separation, were apparently discomfited by the figurative phrase and, perhaps, even sought to suppress the president’s letter. They, like many Americans, feared that the erection of such a wall would separate religious influences from public life and policy. Few evangelical dissenters (including the Baptists) challenged the widespread assumption of the age that republican government and civic virtue were dependent on a moral people and that religion supported and nurtured morality.
Second, a wall is a bilateral barrier that inhibits the activities of both the civil government and religion-unlike the First Amendment, which imposes restrictions on civil government only. In short, a wall not only prevents the civil state from intruding on the religious domain but also prohibits religion from influencing the conduct of civil government. The various First Amendment guarantees, however, were entirely a check or restraint on civil government, specifically on Congress. The free press guarantee, for example, was not written to protect the civil state from the press, but to protect a free and independent press from control by the national government. Similarly, the religion provisions were added to the Constitution to protect religion and religious institutions from corrupting interference by the national government, not to protect the civil state from the influence of, or overreaching by, religion. As a bilateral barrier, however, the wall unavoidably restricts religion’s ability to influence public life, thereby exceeding the limitations imposed by the First Amendment.
As I have previously noted, it is likely that Jefferson's Wall of Separation was referencing Roger William's use of the same phrase where he argued that a wall was needed to protect the garden of the church from the desert of the state. In other words, Williams' view -- one which Jefferson was likely adopting -- was that the wall was only being used to keep the national government from having a corrupting influence on the church by being able to choose one as the church of choice through incorporating a "church of the United States", but was not intended to keep the church from having an influcence on the state. This is consistent with the use of the metaphor in the letter to the Danbury Baptist Association which had been written worried about government encroachment into religion -- not the other way around.
Still, I think the article is well-written and reasonable -- at least more reasonable than the interpretation of the First Amendment being foisted upon us by the courts which virtually any scholar of First Amendment studies recognizes as being hopelessly confused due to the incorrect interpretation of the "Wall" being firm and impassible.