You are correct in saying that no "sect" should be given religious preference, but the founders considered a "sect" to be a sect of the Christian faith.James Madison specifically did not. From Memorial and Remonstrance (1785):
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?
Oliver Ellsworth, a Connecticut delegate to the Constitutional Convention of 1787, in explaining to the people the clause that prohibits a religious test for public office, stated, "A test in favor of any one denomination of Christians would be to the last degree absurd in the United States. If it were in favor of Congregationalists, Presbyterians, Episcopalians, Baptists, or Quakers, it would incapacitate more than three-fourths of the American citizens for any public office and thus degrade them from the rank of freemen."Ellsworth was likely sugar coating the clause for his audience. There were those at the Convention who favored giving Christianity special status. One was Luther Martin, a delegate from Maryland. His words make it clear that his view was a minority view:
The part of the system, which provides that no religious test shall ever be required as a qualification to any office or public trust under the United States, was adopted by a great majority of the convention, and without much debate,--however, there were some members so unfashionable as to think that a belief of the existence of a Deity, and of a state of future rewards and punishments would be some security for the good conduct of our rulers, and that in a Christian country it would be at least decent to hold out some distinction between the professors of Christianity and downright infidelity or paganism.
These were precise men who wrote a precise document that has passed all the tests of time. If they had meant to give Christianity special status, don't you think they would have specifically said so?
-Eric