Actually, there are TWO other Gods Malal and some other bloke whose name escapes me, but the wiki on him was rather interesting.Something Rotten in Kislev
, a WFRP adventure, mentioned two other gods of Chaos, Necoho and Zuvassin. You could assume their existence into 40k if you liked, and why not?
Zuvassin is the god of mischance and bad luck. He has no particular agenda, nor does he do anything really dramatic, he just makes little, irritating pieces of bad luck occur. This can have major consequences - say, a stray bullet hitting a general could change the course of an entire war. As you might expect, very few people seriously worship him.
Necoho is the god of atheism, which rightly sounds ridiculous. He's the patron of the lost or disenfranchised, the faithless and the bitter. His followers almost never actually worship him, due to being atheist and all, but he draws power from them nonetheless. The sort of people who go around putting bombs in cathedrals, that type of person. Necoho is, as you might expect, rather confused. His overall agenda is to destroy the gods and all religion. The WFRP adventure ended with the players destroying a temple to Necoho - the only temple to him in the entire world - which resulted in Necoho appearing to them and congratulating them for striking a blow against organised religion, while also quite annoyed at them for destroying his temple.
Wasn't that silly bit of humanocentric fluff retconned into oblivion, where it rightfully belongs?
Not yet. It can be rationalised to fit into the symbolic loss of innocence of mankind without completely destroying the metaphysics of the Warp, so I'd rather do that than just ignore it.