Without mastering the root of the problem, the Titans could continue to produce opium indefinitely. Even if one or two smuggling routes were cut off, and one or two high-ranking officers involved were brought down, it would not solve the issue. The harm could not be eradicated unless tackled at its source—a point on which Roland and Ji Ai'er completely agreed.
(The problem lies in what comes after.)
Once in possession of the scandal, how would the church use this material? It's likely not going to be made public, to mete out unforgettable punishment to the gangster-like army with justice and righteousness. Instead, it might use this material as a bargaining chip to negotiate with Prince Bernard and involve itself in the conflict for Charlemagne's throne.
It wasn't that Roland was small-minded or paranoid, but the church had too many precedents in this regard, making it impossible for him to trust the clergy—especially those at the higher echelons.