Well, I'm glad she got to this point, but I feel that for such a devoted fan it took too long to realize that her perspective of the world was based on an unreliable narrator. It's a very basic literary device, and the forums for the story should have had loads of people speculating on wether the temple was good or not. Such a devoted fn should have been well aware of all the speculation available, especially as it pertains to wether her favorite character was being manipulated or not.
That aside, the pills do exactly what everyone expected they do, and the pain she felt was what people speculated it was. So that's good. As to why they did it, I can imagine a few reasons. It may be the temple sensed something special about her when she was born, like she was the reincarnation of the original saintess from 500 years ago or whatever, and they didn't want the competition. So they suppressed her. Or maybe they had some reason to want her family line to pass to her uncle (maybe he had contacts in the temple and arranged it himself), so they stunted her mana so she'd be passed over and her inheritance given to her uncle. I still want to learn if her father is aware of what the pills did and was fooled as well, or he was in on it. I doubt it, since he seemed very devoted to her. Also, have we heard about her mother at all? She should be a light element user as well, right?