The Establishment Clause of our constitution makes it extremely clear that the US government may not favor one creed over any other. If O'Rourke had argued to remove tax-exempt status from all religious organizations, that would have been logically consistent and (probably; I am not on SCOTUS!) constitutional.
O'Rourke's assertion that he would seek specifically to remove tax-exempt status from those congregations that do not marry gays and lesbians (but retain it for those who do) seems to fly in the face of this clause of the constitution. To echo what Arnold said, but from an American perspective, that is very, very, very off-putting even to this atheist.
To be clear, as the monitors sometimes need things spelling out, that is not at all because I don't support gay and lesbian marriage. I do! I am just extremely alert to the dangers of government endorsing one form of religious belief or strongly-held feelings of conscience over any other, and exacting penalties against those creeds currently out of favor.
I don't know whether Warren's comment came before or after O'Rourke's during the forum---does anyone know? If it was after, that seems particularly flat-footed.