User blog comment:The Milkman/Indoctrination Theorists Say the Darndest Things, Part II/@comment-24174486-20121204041142/@comment-1440333-20121205195406

You don't brainwash them at all. According to the epilogue you give them their personalities back with Synthesis. Even with Control they have some semblance of individuality as Shepard becomes the new Catalyst/AI, he has no direct control of the Reapers he influences them.