I write this to try and bring more balance to the American Creation blog which, perhaps because of the irresistible temptation, has been doing much bashing of the "Christian America" thesis with myself a prime culprit. Just because David Barton et al. peddle unsound scholarship doesn't mean there is not serious works of scholarship with which the secular left must grapple.
Phillip Munoz of Tufts University is one of the best scholars making arguments against modern, secularist style Supreme Court rulings. The following is a link to an article of his from University of Pennsylvania Journal of Constitutional Law, Vol. 8, 2006, entitled "The Original Meaning of the Establishment Clause and the Impossibility of its Incorporation." You can tell what it's about by the title. Yes, there is a serious scholarly argument (one that, by the way, Justice Thomas endorses) that a proper original understanding of the Establishment Clause makes it impossible to incorporate against state and local governments (the doctrine of incorporation takes various elements of the Bill of Rights and applies them against state and local governments through the 14th Amendment).
Assuming the Munoz/Justice Thomas case is right (it's also one advance by liberal Yale Law Professor Akhil Amar), the story doesn't end. Much of what the Supreme Court currently has the Establishment Clause doing is guaranteeing "equal rights" in the religious context. And the Equal Protection Clause of the 14th Amendment does properly vet a substantive right to religious equality.
For more, see the following with excerpts of Akhil Amar's take on the matter.