One would think that an organization called a mafia would be profit motivated, and I don't see what possible profit there would be in shooting a pair of Christian Missionaries.
No, I think the police chief just wants to avoid looking around his mosque for suspects, either for fear or because he is a sympathizer or worse.
Why do you think they are missionaries? Java is the main province of Indonesia and the name of these people are definitely Indonesian. Instead of thinking these are foreigners working in Indonesia, I suspect they are people whose family originated in Java but for some reason have moved to Sulawesi. There aren't enough clues in the article for me to determine when that move occurred, it could have been several generations ago, nor what the man's teaching specialty is. There are many Christians in Indonesia in all types of professions, many more than the official figures.