Yeah the Faith portions of the game have definitely been the highlight so far.
My main gripe with the game so far is the forced sections where they capture you to progress certain main story missions, it's done so unnaturally and feels totally out of place given the sandbox nature of Far Cry, not to mention how dumb it is that they can capture you at will at any moment, you escape and it just keeps happening.
Other than that, I'm loving it.