I'll let the pro-faith conversation slide as everyone will have a different interpretation mostly due to one's own personal feelings about a particular religion/religion in general.
As far as the references, there is quite a handful, but is that REALLY such an awful thing considering how few original scores come along these days among all the revivals and jukebox shows? What really bothers me more is the pop slant-rhyming in a good 1/3 of the score. "Days/AIDS", "late/way", "butt/c---"...and that's all in ONE song! Perhaps I'm nitpicking a bit with this (after all, Elton John, Eric Idle, Dolly Parton, and Bono & The Edge all did it due to their musical backgrounds), but I do miss the perfect-rhyme purity in musical theatre that Sondheim made a point of defining in all his works.
Incidentally, am I the only one who hears the melody of "Orlando, Orlando, I love ya, Orlando" as "Tomorrow, tomorrow, I love ya, tomorrow"?
...And so, there I was at the stage door for "Equus". The enthused avalanche of "Harry Potter" fans was literally pushing me into the barricades. As I was thrust face-first into Daniel Radcliffe's hat, I suddenly felt the thumb of a lanky gentleman behind me pressing firmly into my back. It was then that I realized that both of his hands had Playbills, and that both arms were outstretched in front of me...