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How about a civil war spy quest line? Like instead of joining the side you want to win you instead join the side you want to lose and act as a mole stealing information and subtly subverting their efforts. It could act as a less of a bad-guy oriented guild for stealth characters.
Many of the civil war had spy-like quests, such as in taking Dawnstar/Morthal pickpocketing the courier, then pretending to be the courier yourself. And what is more spy-like than black-mailing a high-ranking enemy official for information? (Riften/Markarth)
However I love this idea of being a double-agent. I think the civil war was far too short in my books, it could be easily finished in a couple of hours.