To me, when John's father says this, he is referring to the idea that truth can be harmful to people whose faith contradicts those truths. In other words, if you have a faith that says one thing, you can be hurt (spiritually) by truths that contradict what your faith tells you.
In this story, John and his father are (or are going to be) elite priests who know things that the people do not know. They keep some secrets from the people so as not to damage the people's faith. In the quote that you cite, John's father is telling him not to reveal too much truth (all the things he learned when he went across the water) for fear that it will hurt the people's faith.