...... or that the possibility that the Reapers could possibly use the fact that everyone's part-machine to enact "Assuming Direct Control" on a galactic scale if they wished?
I guess you can contrive a way to make this a possibility if you assume that some of what the Catalyst said was a lie and other stuff wasn't, but there's no rational basis for stopping at the point you're proposing here. If you don't know that Synthesis will do what it's supposed to do, how do you know that Destroy will do what it's supposed to do. This sort of thinking leads to Refuse.
Meanwhile, in the Control ending you get to decide that the only way to deal with an insane AI that's got godlike power and has been operating on broken programming for billions of years... is to upload yourself into the system and become the new Master Control Program, despite calling the Illusive Man totally insane when he suggested it, because the road to somewhere was paved with something something, I forget how it goes?
The Catalyst continually working on broken programming for billions of years isn't really a bad thing for Control. It'd be worse if the Catalyst had drifted from its programming. Most of the paranoid fantasies about the Sheplyst going bad start with that.
As for the conversation with TIM, that's a problem with the conversation options. And Sheoard isn't forced to say that TIM's insane, IIRC.
Destroy was bad enough with being forced to sacrifice innocent AI's to take down the Reapers, but it left an even worse taste to realise that you were siding with the bad guys in the other two.
Hey, if that bugs you, don't pick them.