I think the loophole that Nameless found was one of two things:
1. He can't kill Jacob (as said in the beginning of the episode, "you can't kill me unless you find a loophole), but he can get someone else to kill him (Linus).
2. The loophole is him simply taking other people's bodies (which I think is safe to say: Locke, Christian, Walt, all the other ghosts that have appeared on the Island could be attributed to him).
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"A Darwinian attacks his theory, seeking to find flaws. An ID believer defends his theory, seeking to conceal flaws." -Roger Ebert
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