The message in regards to acquiring knowledge can be summed up in John's father's words at the end. When John comes back with this mind-blowing, world-altering news, he says, "Truth is a hard deer to hunt. If you eat too much truth at once, you may die of the truth. It was not idly that our fathers forbade the Dead Places."
He is basically saying that knowledge is good-it gives you strength, power, and sustenance. But you cannot acquire too much at once. If you do, you don't know how to implement it wisely. Instead, learn a little, then learn to use that wisdom wisely in life. Once you have mastered that bit of knowledge, learn some more. John agrees, saying, "He was right -- it is better the truth should come little by little. I have learned that, being a priest. Perhaps, in the old days, they ate knowledge too fast," and this is what led to their demise.
I think that the story is trying to tell us that it is good to have knowlege but when you get too much of a good thing it can end badly.