Bless Me, Ultima is full of witches, healers, god-fish, ghosts, and soul-owls. The supernatural leaves ectoplasmic residue all over this novel. That's what happens when authors delve into what is often called Magical Realism. In Magical Realism, the supernatural often simply becomes a part of everyday life. It's treated no differently than the natural. Magic, in this case, is a part of existence, and while it might frighten some people in the novel, it is not treated as being a figment of one's imagination or something that has been faked.
Antonio never knows how the cross fell from the door when Ultima walked through it, and the Tenorio daughters do suffer after Ultima comes to cure Lucas, so while Ultima clearly represents the power of Good, she is more closely linked to the brujas than might first be obvious.
While in our modern workaday world, we often leave the supernatural to cleverly titled TV shows like Supernatural, in the novel, the powers of Ultima and the miracles of God or the Virgin di Guadalupe are accepted by the most devout characters, as well as those who question their faith.