First, this seems like a lament for the loss of the pastoral and the arrival of modernity. I assume this was a common theme in the era when railroads and cities grew, and traffic and noise arrived everywhere. One can certainly imagine someone saying that a train whistle was loud enough to wake the dead.
Second, I'm not sure how heretical the priest's view of the soul and body asleep is. It's one of those things: what does sleeping in a body for a few hundred or thousand years mean to an eternal soul, waiting for a call to eternal salvation?
Third, at the end, the priest is dead and buried on the hill, along with all the residents of the old cemetery. But, is the countess alive? You debated this. It reads to me like she is, and that she and the count are back together: "For the Count and Countess of Croisac, who adore his memory, hastened to give him in death what he most had desired in the last of his life. And with them all things are well, for a man, too, may be born again, and without descending into the grave."
The style is pleasant to read. I really liked a few metaphors:
"And thereafter, twice a day, at dawn and at night, as the train tore a noisy tunnel in the quiet air...".
""Truly, we were punished enough before we descended to the peace of this narrow house."