Because that's how the war started. The church gained more power with the help of the nobles but then forced all to have faith to this new religion and killing the ones in neutral family like Lippe's family and all regular people that doesn't believe in the church and is singing folk songs.
The plot is a bit messed up now, maybe because its been so long and slow. But, I think it all messed up when the author decided to prolong the toddler age and goes on with the teens age and not just go straight to the point young adult and focus on the problems rather Lippe snatching all the boy's attention.
I loved the idea of her doing everything to save her family and find out their killers but I don't know how singing folk songs is gonna solve that..and there is no further mentions of the spiritual whale(?) That she had obtained.
The story is completely focusing on her trying to make nobles accept folk songs through singing and make a "revolution" as the prince's grandmother said but I don't know how thats gonna be successful. If she manages to make nobles accept folk songs does that mean they're going to change their views on commoners? I think not. They're accepting the "song" not the people so I dont know how singing is enough to make a revolution.