Well, a character in a novel saying that something is a metaphor is not the same thing as the author of the novel saying that it’s a metaphor. Gus’s intellectual grasp often exceeds his reach (he calls a monologue a soliloquy, and misuses quite a few of the bigger words in his vocabulary). But I do think the cigarette is a metaphor, albeit a different one for us than it is for him.
Gus’s idea is that the cigarette is a metaphor for illness, and he keeps it unlit and in his mouth as an expression of his power over illness. “You put the killing thing between your teeth but you don’t give it the power to do its killing.” Gus’s thinking here is that HE has the power. This is why he tends to use the cigarette when he’s feeling nervous or powerless. (He’s also using the most famous commercially available carcinogen to make this statement, so obviously there’s a connection there in his mind: Humans can prevent cancer by not smoking; cancer is something we can have power over; your job is not to give cancer the power to kill you; etc.)
But of course Gus is wrong about all of this, or at least almost all of it. You may have SOME control over whether you die of cancer (you can choose not to smoke), but in most cases humans don’t have control over illness. “You don’t give it the power to do its killing” imagines more agency over illness than we actually have, because in the end much of the fault is in the stars, not in ourselves. So to us, the unlit cigarette is a metaphor for our false perception of control, and our urgent need to feel in control. It’s no coincidence, then, that when Gus’s life is spiraling out of control and he finds himself powerless before fate, he tries (and fails) to buy cigarettes.