Dualism and spiritual beliefs

So, in Duskwall, the main religion (i guess) is the Church of the Ecstasy of the flesh, which is a strange reversal of real-life religious dualism, and views the body as good, but the spirit as evil, or something. this, of course goes hand in hand with the need to destroy ghosts. i assume this is the prevailing spiritual belief.
however, it seems like all the PCs (that i have seen) go counter to this, what with consorting with ghosts, and the desire to become ghosts.
have you ever had PCs that fall on the anti-spirit side? or how have you incorporated this tension of belief into your campaigns?

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