I don't think they're looked down on. To the extent that Sorraine might be, it's more because of poor leadership than because of the Church, which has had some blunders but as Meneldur pointed out, these came about because the Church actually does something.
It is one of the difficulties of 21st century values in a medieval game. The CoS is really the closest thing to how medieval nobles (if not Kings) would think about religion. Most every religion in the Middle Ages was openly hostile to most every other religion, and the exceptions to that rule were more on the local level in the handful of cities where you had multiple faiths mostly getting along -- like Jerusalem, until the Turks came in.
As a player I wish there was some sort of middle ground to pursue, because religion should be one of the prime movers of conflict in the game. But no King who enjoys a firm level of control is going to willingly hand over control to any religion, so Galiard can't do much about it, and the other faiths are too fragmented (at least at the moment).
Most of the realms on the FEI have been secular dictatorships of one form or another and they'd be pretty foolish to give that up.
