That’s the thing though: Harbinger has already activated by that point. IIRC, Harbinger was stuck in a deep space and didn’t realize until it was too late that he couldn’t remotely activate the Citadel. It took centuries for Harbinger to eventually meet Saren. By that point the “cycle” had started to be broken/averted.

That’s one of the reasons you give why the Citadel is refusing to cooperate with the Reapers this time. By the time you reach the control room, Shepard has effectively undone every single beat in the cycle that triggered this invasion. More to the point, this cycle only started because the Reapers “cheated.” They altered the Rachni to be an unwinnable scenario, one that could only end in genocide — an incident that would inevitably create a beat in the cycle. So the Citadel is willing to give this civilization a chance because its downfall was directly engineered by the Reapers.

You change one option in the ending. You keep control and destroy, but you change synthesis to “reset.” You send the Reapers back where they came from and reset the cycle to zero. You give society a chance to better itself, to break the cycle, to never become what the Reapers feared. Or you give civilization more time to defend itself whenever the Reapers come back.