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The codex describes the Penitent abilities as a save vs. psychic powers directed at the Inquisitor OR in if the Inquisitor is in the area of effect. Storm caller from the space wolves librarian protects the squad it is cast on with cover status. Of course that effect will be felt by the Inquisitor unfortunate to be in the path of the drunk charging puppies the following turn. Can the Penitent stop this power like a hood could? Is there a specific range attached to it in some FAQ/post, etc.? I'll assume no, but you never know if GW made a rule adjustment.
How can the inquisitor be affected by storm caller? If the wolves charge storm caller doesn't work and in CC you don't get cover saves.
I don't see how that would work but you are right, a pentiant can't stop it as it won't directly affect the inquisator (and the area of affect is the squad so he cannot be affected as it isn't a template ability)
Short answer: no