The goblins are a foolish race, they glorify immediate power, and chaotic actions. A god that is silent and invisible is only popular to the goblins while they have no alternative. Once the absolute steps in, it grants goblins mind control powers and makes them stronger. Hence the goblins joined with them- a lot of goblins can’t leave as the mind control is like the imperious curse in HP.
On the topic of playable goblins, I think I would not work. Goblins are not always evil, but I can not think of any instance of games where goblins would be shown as good. Even Styx from Orcs and Men, is not good yet willing to work with humans. Maybe if you played a backstabbing wretch that only did it for gold? I also find it unlikely that a nobody goblin would be kidnapped by the mindflayers as we know they kept them where they did.
