All you need to do is tweak the DoT perk. Add the caveat "to minions of darkness". That way, DoT only activates against PvE enemies. It would be the same as those helmets that only give you more super energy against minions of the darkness.
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So then, why would Thorn be an exotic with a quest? I mean, if you take away its 'exotic' perk, its just another handcannon, right? Or are you suggesting the Bungie go through and remove all PVP related perks on weapons?
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Did I say remove it? I actually said add to it. Like the Knucklehead Radar helmet, which says "More Super energy from non-Guardian kills." Add that "non-Guardian" part to the end of the Thorn's Mark of the Devourer perk, et voila, it's fixed. It's still a 3 shot kill. It's still got crazy good range. In PvE it would stay exactly the same.
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I'm pretty sure, though there is a reasonable chance that I'm mistaken, that "Minions of the Darkness" applies only to the Hive and Vex as those are the only two who serve the Darkness, whereas the Cabal and Fallen are seen as running from it. So no, that wouldn't necessarily work. But I get what you mean.