In the prologue the priest explains to the penitent that he also was a murderer. The rest of the book is the priest's autobiography, and no, that particular crime isn't the climax of the story. The beginning of the story is set in a monastery in Cuba a few years from now, and from the fact that the cover shows a pirate at the helm of a sailing ship you can guess where the rest of it is set. Don't look for an explanation of the transition. After all, it might all be just his imagination, right?
Wolfe did a lot of research when he wrote the book, and it flows quickly and cleanly. A lad alone in that environment wouldn't have many options, and after a mischance or two his direction is fixed. On the other hand it isn't at all obvious how he's going to become a priest at the end of it--until the end.
Read it. Maybe you'll find it for a penny plus shipping at Amazon too.