Lets not forget that Reaper Indoctrination is based off of the Leviathan's own form of mind control. This make it apparent that trusting either one of these critters (Reapers or the Leviathan) is incredibly naive.
Plus geth in ME1 were only attacking the human colonies because Sovereign said so(with Sarens help), and it is quite likely that they have done the same trick before turning the Starbrat's words that the synthetics will always attack organics kinda like a self-fulfilling prophecy since they are manipulating them to attack. its like saying "the glass will break" and then dropping it so that it will.
I know I am attributing more to the Reapers, the damn AI and the bioware more than they probably thought but this way it makes sense.
The reaper control AI cannot kill Shepard in that chamber, the Crucible is preventing it from acting on that so instead it opts to mislead Shepard, make it seem like the option he came here for is not worth it and that the other two options presented are a better path. After all it knows shepard would sacrifice himself if needed.
The other options are traps, Control uploads the mind of Shepard into the runtimes of Reapers, possibly influencing them enough so that they stop killing, but at the same time the AI is preserved and it could try with the help of now trusted Reapers to mold the galaxy in the way it wants like the Leviathan of old, as with synthesis its pretty clear to me that its what it wanted from the start, a stop to random biological evolution, everything now in a form that it and the Reapers can control. Everyone gets indoctrinated without knowing it, without feeling it, so no one would question. Finally the galaxy is in the image of the Reapers.
Which is why the whole thing about geth destruction and EDI could be and probably is just a lie. Energy waves destroy hardware not software and since both EDI and geth do not have reaper hardware then they would survive, all it would do to them is probably shut them down temporarily, like a power surge would.