Odd. I swear I remember posting in this thread, but the forum search turned up nothing. Guess it's time to correct that!
As with many things, whether you use "evil" gods, or "everything's grey" gods, or "gods are good, but demons/devils/etc. exist," or even "gods are evil but other supernatural powers can be good"...these are all tools. The most productive thing is to go in clear-eyed, with intent and conviction.
Personally, I like the idea of "evil" gods that are still useful, even necessary, because that forces a tension that I think gets bled out by having everyone always be equally ambivalent/grey-and-grey/etc. Such approaches just make it hard for me to really care about any of them. Especially if it actually verges on being black-and-black morality as is so popular these days, as TVTropes says, "Too Bleak, Stopped Caring."
But if you're going to do this, you really have to know what you're doing. And yes, there is the issue of "OUR gods are good, THEIR gods are evil," but even that isn't always fitting a given pantheon. The Egyptians had Set, aka Sutekh, who was pretty bad and often genuinely vilified by the Egyptians themselves, but also represented the ability of the deep desert to protect Egypt from its enemies. Or the actual Tiamat, who was both a progenitor goddess (the primordial salt-ocean, alongside Abzu's primordial freshwater) and a mother of horrible monsters who would defend any of her children...including the ones extremely keen on eating mortals by the dozen or whatever.
Part of why I like this is also that I'm pretty partial to the idea that true deities (as opposed to simply powerful supernatural beings that ordinary mortals revere or worship) are metaphysically linked to or embodiments of their core concepts. Tiamat (the D&D one) is not just a powerful supernatural being that happens to be able to grant powers related to strife, vengeance, greed, and tyranny. She actually embodies these things. Which means, to truly slay her is to truly weaken these abstract concepts within the world. Just as these things exist independently of her, her destruction cannot end them forever, but the world is in fact a kinder, more forgiving, more just, more generous place if she is destroyed.
Yet such destruction necessarily has knock-on consequences, both instrumental (sudden power vacuums are always...problematic at best) and inherent (you just killed one of the few gods that survived the Dawn War, and perhaps more importantly, one of the few gods who could be relied upon to rally "evil" against "oblivion.") Hence, even evil deities have uses and may even be "necessary" in some sense. Thwarting without eliminating can in fact actually be the wiser choice. That's deeply interesting to me, because it means even deeply committed "always do good, never do anything that smells of Dirty Business" characters need to really think and put in cognitive, moral effort rather than just coasting on "be nice and kick evil's butt."