By the time the Church took over, the city and its citizens were already loyal to the religion and it's beliefs.
Before the church came to be the city was completely under the control of the house Barkemy who ruled with an iron fist. They ensure the imperial laws are followed in the city which made this house one of the most loyal in the Imperial Government.
That is also why the Imperial Government accepted many requests from the church impersonating as the Baron.
Because they believed the baron and his kin to be the most loyal so in no way a betray could occur though there were doubts regarding as to how a religion appeared in this City.
The Church's charitable contributions made them look not evil. That is the only reason why the church was never under scrutiny.
The citizens before the Church weren't much liking to the house. They were sceptical, doubtful and secretly hated their previous lords. The church atleast gave free things for belief.
