It's for this reason that I liked the idea introduced in 4E that made Asmodeus and Lloth gods. With the game itself seemingly putting the idea of the gods above all the other potential enemies of the heroes... making at least a few of those devils and demons actual gods rose their groups up and gave them a bit more weight in my eyes personally.
As I've bandied about ideas for my own potential campaign world in the past, this question came up enough times that I tried a system wherein there weren't any pantheon of gods. Instead, there was one single unaligned overdeity that wasn't worshipped per se (a la Ao), and then all the beings actually worshipped by the peoples were the pantheons of Archangels (LG), Archfey (CG), Archdevils (LE) and Archdemons (CG). Each of them had their own domains they controlled and there wasn't a lot of overlap between them.
Since I've never actually run any games in my own setting (I keep using the existing ones already created because I'm ultimately lazy) I haven't seen how they work out in play. But I did like the idea that "evil cultists" were the devil worshippers and demon worshippers, not the ones who found divinity in storms or the ocean just because Talos and Umberlee were made "evil" for whatever reason.
4e was not the fist though, take Iuz, his demonic rank is that of a cambion, still on Oerth he has the powers and rank of a demigod, including the ability to grant spells to his followers. (2e)