Arian:
I respectfully disagree. DESTROY requires you listening to Starbinger and thinking that at least part of it is true. After all, you have to accept that he's telling the truth at least a little. After all, how can you choose unless you know what each choice does? Also, again, you never tell Starbinger that it's possible that he's wrong. You're also ACCEPTING A SOLUTION THAT HE OFFERED. You don't do that in Reject. You ignore everything he says and just tell him to GTFO. You stand up for what you believe in (Free will) and say that you will never, ever compromise with the Reapers.
And the vast majority of what Harbinger wants Shepard for is the fact that he's an icon. In fact, he'd probably want a broken Shepard. That's a bigger blow to morale than a traitorous Shepard. A traitorous Shep would become a martyr, since the real Shepard fought the Reapers until the very end, and now the Reapers would pay for what they did to Shepard. A broken and hopeless Shepard, however, would cause the troops to lose hope and despair. And, honestly, look at his speech. Does that Shepard look broken or like he's "lacking conviction" to you? Or does it look like he's taking more of a stand and doing something harder or more costly than any of the other choices?
Again, Reject is not just rejecting Starbinger's options, it's rejecting everything the Reapers are and everything they stand for. When you choose Destroy, you're trying to achieve what you view as the best future. The Reapers are master manipulators, as you have pointed out, and anytime you fight FOR something (Even a future free from the Reapers) I'd say they could turn any cause into some way to help them. For Reject, you are saying that no matter what, you will never surrender or compromise with the Reapers, and all the choices are compromising with the Reapers, even Destroy, since Starbinger presented the solution.
And to address another of your points, regarding Shepard choosing an option that isn't presented by Harbinger, Arian, I finish with a quote from Dream Anderson said not 5 minutes before this conversation: "There's always another way."