You might be interested to read a bit of legal analysis of the First Amendment, including the three tests used by the courts to determine violations of the Establishment Clause:

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The first two standards were part of the same formulation. 'The test may be stated as follows: what are the purpose and the primary effect of the enactment? If either is the advancement or inhibition of religion then the enactment exceeds the scope of legislative power as circumscribed by the Constitution."

I think a case could be argued that the primary effect of the FMA would be an advancement of religion, especially if the proponents of the FMA clearly state that religion is the basis for the content of the amendment. Now, these tests are applied to legislation, not constitutional amendments, but it would leave us with amendments that would arguably be at odds with each other.

Here's a nice quote from Jefferson, too:

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In 1802, President Jefferson wrote a letter to a group of Baptists in Danbury, Connecticut, in which he declared that it was the purpose of the First Amendment to build ''a wall of separation between Church and State.'

--Dan.