Qualia is an existence before Amon. Amon only became God because Qualia destroyed the whole world.
Amon needs prayers to remain as a God, which is why he created the Rites of Resealing system.
If he creates the Qualia, then it would kill everything. Which in turn means that Amon loses support and dies.
Qualia is stronger and can kill Amon. They're different existences. Amon wouldn't have gone through the trouble to create Lessica and the Four Horsemen if he could get the Qualia to just kill every single human anyway. It just doesn't make sense.