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You can't get more originalist on the Establishment Clause and the separation of religion and state than quoting James Madison, author of the Bill of Rights.  The following are excerpts from Madison's Memorial and Remonstrance Against Religious Assessments.

On the effect that established religion has on people within the state and advancement of society:

Because experience witnesseth that eccelsiastical establishments, instead of maintaining the purity and efficacy of Religion, have had a contrary operation. During almost fifteen centuries has the legal establishment of Christianity been on trial. What have been its fruits? More or less in all places, pride and indolence in the Clergy, ignorance and servility in the laity, in both, superstition, bigotry and persecution. Enquire of the Teachers of Christianity for the ages in which it appeared in its greatest lustre; those of every sect, point to the ages prior to its incorporation with Civil policy. Propose a restoration of this primitive State in which its Teachers depended on the voluntary rewards of their flocks, many of them predict its downfall. On which Side ought their testimony to have greatest weight, when for or when against their interest?

On the threat that established religion poses to liberty:

Because the establishment in question is not necessary for the support of Civil Government. If it be urged as necessary for the support of Civil Government only as it is a means of supporting Religion, and it be not necessary for the latter purpose, it cannot be necessary for the former. If Religion be not within the cognizance of Civil Government how can its legal establishment be necessary to Civil Government? What influence in fact have ecclesiastical establishments had on Civil Society? In some instances they have been seen to erect a spiritual tyranny on the ruins of the Civil authority; in many instances they have been seen upholding the thrones of political tyranny: in no instance have they been seen the guardians of the liberties of the people. Rulers who wished to subvert the public liberty, may have found an established Clergy convenient auxiliaries. A just Government instituted to secure & perpetuate it needs them not. Such a Government will be best supported by protecting every Citizen in the enjoyment of his Religion with the same equal hand which protects his person and his property; by neither invading the equal rights of any Sect, nor suffering any Sect to invade those of another.

On the fact that establishing a broad class of religions inevitably permits the government to narrow its focus and establish one particular religion or one particular sect of one particular religion:

Because it is proper to take alarm at the first experiment on our liberties. We hold this prudent jealousy to be the first duty of Citizens, and one of the noblest characteristics of the late Revolution. The free men of America did not wait till usurped power had strengthened itself by exercise, and entagled the question in precedents. They saw all the consequences in the principle, and they avoided the consequences by denying the principle. We revere this lesson too much soon to forget it. Who does not see that the same authority which can establish Christianity, in exclusion of all other Religions, may establish with the same ease any particular sect of Christians, in exclusion of all other Sects? that the same authority which can force a citizen to contribute three pence only of his property for the support of any one establishment, may force him to conform to any other establishment in all cases whatsoever?
Now why did Madison and the other founding fathers place such a great emphasis on the separation of religion and state?

As the words of Madison suggest they were cognizant of history and well aware of the religious wars that tore Europe apart and destroyed liberty.  They wished for America and the new republic we established here to avoid those plagues.  They understood that Americans were, by in large, a religious people.  They understood public profession of religious beliefs is essential to respecting the dignity of human beings and preserving liberty, but that the moment government interfered both dignity and liberty were threatened.

Beyond the fundamental right to freedom of conscience, the founders understood that right was not truly protected so long as government became arbiter in matters of religion.  Therefore, the founders determined to separate religion and the state.  As Madison wrote:

We maintain therefore that in matters of Religion, no man's right is abridged by the institution of Civil Society and that Religion is wholly exempt from its cognizance.
Should the Hobby Lobby case be decided for the company, then this would make the law of the land exactly what the founders intended to avoid.  Government would now become the arbiter of religion.  Government would decide what is a sincere religious belief and what is not a sincere religious belief.  Government would decide which religious beliefs merit exemptions from the law and which religious beliefs do not merit exemption from the law on a sliding scale based upon its evaluation of religious doctrine.  This is a very dangerous path.

Now, this is not to say that there are certain instances where religious beliefs supersede otherwise applicable law.  For example, a Baptist church can rightfully limit its search for a new pastor to only those that are ordained by a Baptist seminary, just as a synagogue can rightfully limit the search for a new rabbi to those that received smicha (ordination) from an institution it recognizes.  Note, however, the common thread that exists here.  These are religious institutions acting in their religious capacity; they are not for-profit corporations seeking to evade obligations under the law by way of claiming religious liberty.

A little originalism would go a long way here.

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