To quote The Avengers:"Why am I back? How did you get him out?"
"Cognitive recalibration. I hit you really hard in the head."
More sensibly, some kind of purification ritual would seem appropriate. To start with, look at anything that comes up in exorcisms and 40k it up a bit. It might include pain purification (i.e. torture, of a sort), partial or total mindscrubbing (possibly chemical, possibly psychic), reading of holy passages (or having them tattooed onto the skin), exposure to sacred objects... that sort of thing.
Really depends on how deep his Inquisitor thinks the taint runs (evidently not enough to have just shot him).
although this seems out of character for a recongregator who believes that the ecclesiarchy is deeply corrupt
Believing that the Ecclesiarchy is corrupt doesn't have to mean that one thinks all priests are corrupt.
One of my characters believes that corruption is rife throughout the entirety of the Imperium. This does not however mean she thinks every single Imperial citizen or servant - every lowly Arbitrator, Priest, Guardsman, etc - is dodgy.