The Catalyst analysis is faulty. It underestimated the resourcefulness of organics. This cycle just banged together some stuff others designed and got a Crucible out of it, a device capable of fulfilling the Catalyst´s ultimate "desire" and kill synthetics in one handy device. if the Catalyst had let the more knowledgeable builders survive and made them aware of this "problem" instead of wiping them out, the problem would have been solved long ago. And it never provided hard data, which was reviewed or scrutinised. All of that could be based on pure belief and as ridiculous as geth worshipping a Reaper, sooked up by an AI with buggy code.
The spacefaring species of the galaxy have to die because some dude is utterly convinced that they have to. It never showed anything that makes it more than a silly philosophy religion, ideology or whatever label you want to slap on it.
As I wrote earlier in the thread, the Catalyst is telling you the truth. The Catalyst has no motivation to lie to you, because the Catalyst is *asking your opinion* on what to do with the Crucible, because the Crucible is ultimately under the Catalyst's full control. (The Alliance just handed a loaded superweapon to the AI that oversees the enemy, after all -- which was installed aboard a station that they knew was built by the enemy and full of surprises. Desperate times, I guess?)
Low EMS endings indicate that the Catalyst isn´t actually in full control of itself. If Destroy is the only possibility, it clearly resents it and still points you to the right direction, raising the platforms to go there in the process. As the Ai says itself, destroying synthetics won´t help, as peace won´t last. And it clearly had a preference which wasn´t Control or Destroy.
And the thing still needed you. If you refuse to decide, it just goes on with the harvest. So it doesn´t say, uh well, if you don´t like to jump into the green beam, I have total control anyways and activate synthesis now because I don´t lie and synthesis is awesome. The catalyst had clearly stated opinions what it´s preferences are.
So nope, no Catalyst with full control.