User blog comment:The Milkman/Indoctrination Theorists Say the Darndest Things, Part II/@comment-98.240.62.123-20121205061803/@comment-24174486-20121205125511

Look at Saren, look at the Illusive Man. Did the Reapers make them want to do what the Reapers wanted to accomplish? No—the Reapers manipulated them into believing that they were furthering their own goals. Saren continued to believe that assisting the Reapers would convince them to spare galatic civilization, and the Illusive Man sought to control the Reapers so that he could elevate humanity's position in the galaxy.

Based on that, if the Reapers truly were trying to indoctrinate Shepard and Destroy is invariably the option Shepard would want to choose, why don't the Reapers use Shepard's desire to destroy them to manipulate them—lead them to believe that their actions would result in the destruction of the Reapers when in reality it wouldn't help at all?

The Catalyst simply gives you its opinion on the options at your disposal. In fact, without a high EMS, the option it advocates isn't actually possible. It does not stop you should you decide that the option it likes the least (Destroy) is what you choose. Control doesn't exactly "help them"; whether or not Shepard taking over the Reapers would impact the balance of organic and synthetic life all depends on Shepard's personality and beliefs.