Too controversial, and in Civ4, it was basically a diplo mechanic. It served no great strategic purpose, and was not selling more copies of Civ. I'm not surprised at all that it got ditched.
I don't think it's likely that a good Religion mod will be made for Civ5. Too many people want a really complex religion mechanic (More complex than Revolutions are now), and that would take forever. The other spectrum (me) wants a simpler, but flavorful religion mod. I just can't see this dichotomy ever comprise. It's why I have avoided Religion Modding in Civ4.