Can quinoa be used as a soup thickener?
Cooking grains in soup is an effective way to thicken it, but quinoa is probably not the best choice. Quinoa has saponin in it, a bitter tasting phytochemical which has been known to irritate the stomach. Much of the quinoa sold has been presoaked to get rid of much of the saponin, but some may remain which is why you boil it separately and discard the water. If you put quinoa in the soup any traces of saponin could ruin or at least add off flavors to the dish. 

Rice or barley would be my first choice for that sort of thickening, they take longer but they don't impart much flavor to the food. Couscous is faster, but would give the soup a grainy texture. Giant couscous may work okay, I've never tried it in a soup myself.