Yeah, they're kind of a Catholicism stand-in, so pretty much all the things that suck about real life organized religion is stuff that also sucks about them.
You do lose morality for killing Saints, and in certain parts of the game they're friendly with you in an "enemy of my enemy" kind of way, but given that morality, as a stat, is clearly more synecdoche for "reputation [with the local authorities]" than it is any kind of spiritual morality/karma, it's pretty clear that they're meant to be bad guys overall. Especially with how they're involved in certain side-quests.
On a COMPLETELY UNRELATED NOTE that has ABSOLUTELY NO BEARING OR RELEVANCE to ANYTHING I JUST SAID, Cocona is a perfect cinnamon roll of innocence and goodness, and if anything were to happen to Cocona I would deliver unto Noer and all the major ports the same devastation that struck Sybaris, sparing not one of the miserable fuckers who, even if by mere inaction, allowed that harm to come to her.
I would ALSO LIKE TO STATE that there may have recently been a massacre that took place at the Saints' Chapel north of Noer, and that this massacre has NO RELATION WHATSOEVER to anything I've said here―though if you choose to connect the dots and infer relevant information that should be incorporated into your self-preservation instincts, I bear no responsibility nor obstacle.