This blog by a PhD student contains a useful legal analysis of the demand that a conscience clause be included in the Civil 
Partnership Act.
The author, Eoin Daly, appears to be unsympathetic to such a demand, but he nonetheless believes that it might have a strong constitutional basis and he cannot understand why this possibility was so lightly dismissed by State lawyers and their political masters.
He points out that in the one and only Constitutional case that dealt with the question of religious freedom and the general applicability of laws, ‘Quinn’s Supermarket v Attorney General’, the Supreme Court was very sympathetic to religious freedom claims.
In this case, renowned Supreme Court judge Brian Walsh said that: “Any law which by virtue of the generality of its application would by its effect restrict or prevent the free profession and practice of religion … would be invalid having regard to the provisions of the Constitution, unless it contained provisions which saved from such restriction or prevention the practice of religion of the person or persons who would otherwise be so restricted or prevented.”
This is fairly broad and on the face of it indicates that the Civil Partnership Act should have contained a conscience clause, or at the very least, that President McAleese should have referred it to the Supreme Court.
Daly also believes that the conscience claims of Christian public servants should have been accommodated easily enough without denying same-sex couples any of the services to which they are legally entitled.
He suspects that the real reason for the rejection of a conscience clause is that the politicians in question strongly disapprove of the religious belief in question. Daly himself approves of this belief, but he is honest enough to concede that the rejection of a conscience clause might be “rooted, almost subconsciously, in the teleological hope of radical social transformation,” in other words, a desire to force those who disapprove of homosexual activity to approve of it through legal force.”
Precisely.