You only keep the Reapers enslaved, which according to common perception is justifiable.
How so, if they were never truly responsible for their own actions?
If they wanted to continue the harvests or otherwise attack and kill people even after freed from the Catalyst, then it would be justifiable for AI-Shepard to "assume direct control" and prevent that, but the Synthesis epilogue suggests that they wouldn't do that. I realize that the Synthesis epilogue never happened in a universe where Shepard chooses Control, but insofar as it tells us something about how Bioware conceives of the Reapers and their likely actions if given independence, I think it's still relevant evidence.
I'm not really anti-Control - I'm still trying to make up my mind about whether I'll choose Control or Synthesis when I finish my current "canon" playthrough (hopefully by the end of the week), but for a Paragon Control ending, I have to imagine that AI-Shepard is leading the Reapers by consensus rather than micromanaging their thoughts and actions.
One thing that's interesting about Control is that it's probably the most open-ended of the choices, in that we can imagine all these different possibilities for what AI-Shepard eventually does. The eventual shape of the Synthesis techno-utopia is left vague, I suppose, but there won't be a single individual with extraordinary power to steer things in one direction or another. Refuse and Destroy are pretty straightforward - Refuse means the current civilizations lose the war, Liara's time capsule is buried somewhere, and the next cycle somehow puts a stop to the Reaper harvests, and Destroy means synthetics are wiped out and the surviving organics rebuild through conventional means.