Also the Church itself isn't as looked down upon as you make out; it has a significant presence in nearly every northern realm and no ruler has yet attempted to ban or destroy its temples (though if the Church dosn't get its diplomatic ability back on track then that could change).
That's actually not entirely true, during the last war, Zonasa authorized the burning of Sartanian temples after they burned temples in Zonasa (it was not particularly encouraged, just allowed -- normally such an act might get one banned), and after another event, Morgan strongly considered banning CoS -- he had the support of all the lords to do so, in fact, he just decided not to in the end.
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.
I think to some extent that this may also be because in general, most realms have multiple religions in them, and there is certainly no huge religion that has pretty much sole claim to several realms the way Christianity and Islam did in our middle ages, or how SA does on Dwilight. And so avoiding internal strife caused by followers of the other religions probably keeps some rulers from trying to advance their religion too much. That has always been Morgan's reasoning behind Zonasa's official policy of religious tolerance (I'm not sure that's how it started, but it's why Morgan thinks it's a good idea and hasn't tried to stamp it out) -- and why we've actually executed someone for stirring up religious unrest.
And this is precisely why a smart King should be very, very religious. If you are in charge of a Church, then you can have influence wherever it does...Which might be well beyond the boundaries of your realm.
This can be a double edged sword, though, in that then the religion may more easily influence your realm . . . so it depends how much risk you want to take and how confident you are that you will exert more influence on others than is exerted on your realm . . . if you're confident in that, though, it is generally the way to go.
