Malin spoke of certain individuals, those being the zealots. Once they knew these secrets, Malin realized he had to protect everything; otherwise, there would always be trouble—if he revealed it all, the zealots would regard Malin with the same hostility as followers of the Evil God, seeing him as a thorn in their side.
Of course, this situation was not really troublesome for Malin—from a faith perspective, Matilda was a believer in the Lord of Justice. She certainly knew the Truth, and it seemed the Church of Justice didn't spread the Truth around the world, so Malin trusted Matilda's discretion.