This was his conceit. It was his mistake to make, it was a false belief.
He did of course play his part in getting Donnie escaped, but in the Reverend Orisons mind... It was a holy mission, he believes he was sent by God. And he he actually believes that he was the one to deal with Donnie Pfaster.
He wasn't.
This is to say that Orison is a not just a very powerful person, there is no doubt about that- But he really believes... he really thinks he is hearing instructions from Ghod Almighty. If this were true, the episode would have ended in that plot of dirt where he takes Donnie.
We have to ask ourselves if we think that the Reverend Orison was surprised by this development? It's the same as when we hear about famous televangelists being indicted for federal crimes and imprisoned. They literally believed that "God" was telling them to do whatever it was, which turned out to be illegal... and they still believe it to this day even after being released from prison. And they are still doing it.
It's the same as what Orison is doing, although he excuses himself by telling Skully that she doesn't need to worry about certain convicted murderers as they are now "with God". This is an extremely conceited and false purpose.
He had already tested this conceit twice on inmates. That he was successful with those convicted murderers does not mean he could have been able to "punish Pfaster in Ghod's Name". Pardon me but my interpretation of the Bible, when it talks about vengeance is that even if you (Believe you have) have some kind of license given to you by God to perform "His" vengeance, it still does not empower you to break the laws of man in order to do it. And anybody claiming to be doing God's work where it crosses a boundary line of law is deluded... and that is simply to put it mildly, The reality is much worse.
It was Skully all along. If you want to interpret this episode as an "X-Files prophecy", she was the one chosen by God. She was the only one who had the "authority" to do it.
The Reverend Orison thought he was dealing with another man. But we already knew the nature of Donnie Pfaster from the first episode he was in. And although his actual nature was played down in "Irresistible", there were two people that saw him for exactly who he was: his former boss at the funeral parlor, who yells "get out of here, you FREAK!", and Skully of course sees this same image. And we know that it rattled her down to her bones.
So when this X-File begins and brings up the prospect of dealing with Pfaster, she is visibly disturbed.
At the same time, she is being comforted and instructed by repeatedly hearing the song "Don't look any further", performed here by John Hyatt with a very "spooky" guitar solo. On one hand she is comforted by the song, on the other, it gives her the strength to continue working on the X-file, but the song also gives her the direct authority to handle Pfaster, to accomplish what the Reverend Orison absolutely did not have the power to do.
And this is what that final silent scene in this episode means.
As Skully asks herself who it was, that was working in her? We know that it could not have been anything evil.