I find the "mostly" important there. To borrow the cult of the rat queen example, that's the kind of thing that most people don't approve of, but I let the PC's chart their own course through the muddied waters of motive. Do they track down the cult and slay them because they're horrified at human sacrifice? Maybe because the mayor wants the killings to stop, and pays in gold? Because a friend or relative was sacrificed? Because the Rat Queen is clearly subservient to the God of Vermin and Rot worshipped by the PC's, and these heretical upstarts must be taught a lesson (so yeah, clearly, I'm okay with PC's of pretty ambiguous morality)? Because they really like killing things and taking loot, and the guards will encourage them murdering the cult instead of merchants?
That's for them to decide. Even if the PC's aren't heroes, they're still the stars of the show. I'm just here to window-dress their stories and make some outside conflict occur.
Edit: As Crothian posted while I was typing mine, he made a point I hadn't thought of. The gods are either Good (defined as, if not in fact benevolent, at least not hostile to mortal life) or Evil (hostile to the concept of mortal life, wishing them only misery and pain). Mortals, however, unless they bring those essences into themselves (by being able to cast divine spells), are just mortals, like playing pieces on a board. You can't Smite the burglar or the tax collector, but the Priests of the Void are itchin' for holy anger.