Okay, so theory time: I think the reason they are hiding the MC's mana is because they are jealous(?) of her light magic and her mana that may be more than a speck. It might even lead to the story of the first Priestess whatsoever 500 years ago. I think, the father knew about the pills because it's impossible to ignore the fact you're giving a medicine to your daughter without knowing what is it and especially since he has a connection with those 'good' persons. And the reason the temple is happy of their marriage is because MC's light element will be gone since light magic was said to be recessive, thus it will no longer be a threat(?) to them. Also, Deborah may really be deceiving Abel in the novel.
Woah, this is my first time making such theories... anyways they're just theories.