Well, since the digs and asides aimed at religious establishment begin with paper #1, I suspect you aren't falling all over yourself in your headlong search. Here's a ref:
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December 8, 1787
The Federalist Papers
Federalist # 19
The Insufficiency of the Present Confederation to Preserve the Union
Alexander Hamilton and James Madison
So far as the peculiarity of their case will admit of comparison with that of the United States, it serves to confirm the principle intended to be established. Whatever efficacy the union may have had in ordinary cases, it appears that the moment a cause of difference sprang up, capable of trying its strength, it failed. The controversies on the subject of RELIGION, which in three instances have kindled violent and bloody contests, may be said, in fact, to have severed the league. The Protestant and Catholic cantons have since had their separate diets, where all the most important concerns are adjusted, and which have left the general diet little other business than to take care of the common bailages.
That separation had another consequence, which merits attention. It produced opposite alliances with foreign powers: of Berne, at the head of the Protestant association, with the United Provinces; and of Luzerne, at the head of the Catholic association, with France.
Publius
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The federalist has about a dozen of such references indicative of the paranoia many of the founding fathers harbored for the poisonous combination of religion and state interests whose european cavalcade of horrors was far fresher in their minds than it is in ours.
Their fear was not that references to religion would be made in public education - a system which had not yet been unconstitutionally foisted upon the public -- but in regard to the establishment of a specific denomination or church body as the official religious body of the United States.
The Dover school boards actions are so far removed from what Hamilton and Madison were discussing as the distance between galaxys.
Your interpretation of the "separation of church and state" would ultimately prohibit anyone who believed in God from holding public office or even voting.
... nothing could be more ill-judged than that intolerant spirit which has, at all times, characterized political parties. For in politics, as in religion, it is equally absurd to aim at making proselytes by fire and sword. Heresies in either can rarely be cured by persecution. [Federalist #1]But there's a lot more in Federalist #10:
The latent causes of faction are thus sown in the nature of man; and we see them everywhere brought into different degrees of activity, according to the different circumstances of civil society. A zeal for different opinions concerning religion, concerning government, and many other points, as well of speculation as of practice; an attachment to different leaders ambitiously contending for pre-eminence and power; or to persons of other descriptions whose fortunes have been interesting to the human passions, have, in turn, divided mankind into parties, inflamed them with mutual animosity, and rendered them much more disposed to vex and oppress each other than to co-operate for their common good.
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It is in vain to say that enlightened statesmen will be able to adjust these clashing interests, and render them all subservient to the public good. Enlightened statesmen will not always be at the helm. Nor, in many cases, can such an adjustment be made at all without taking into view indirect and remote considerations, which will rarely prevail over the immediate interest which one party may find in disregarding the rights of another or the good of the whole.The inference to which we are brought is, that the CAUSES of faction cannot be removed, and that relief is only to be sought in the means of controlling its EFFECTS.
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By what means is this object attainable? Evidently by one of two only. Either the existence of the same passion or interest in a majority at the same time must be prevented, or the majority, having such coexistent passion or interest, must be rendered, by their number and local situation, unable to concert and carry into effect schemes of oppression.
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A religious sect may degenerate into a political faction in a part of the Confederacy; but the variety of sects dispersed over the entire face of it must secure the national councils against any danger from that source. [Federalist #10]