The only indoctrinated agent we have seen was TIM onboard the citadel
I don't think he conquered the citadel alone... but the citadel could have been taken by the reapers alone, why not.
After the reapers had taken control of the citadel, why shouldn't they remove the prothean alterations? That trick caused them a relevant amount of hassles...
. I mean, you only want to communicate the most important things in the story, obviously the sabotage was a very important measure and was communicated in ME1 as it was central to the plot. In ME3 there is no such citation of it being reverse thus we have no idea and cannot conclude it was, nor even that the sabotage impacted the arms.
We are discussing about that a lot, and we are dissecting every cut-scene and every citation, so probably our perspective is a little bit distorted.
But really, given the plot of ME3, it's pretty irrelevant who/where/what is able to control the citadel arms and the mass relay.
I know many people that have played all the ME trilogy and none of them had risen questions like "if the citadel is part of the catalyst, how is it possible that catalyst is controlling the magic elevator and/or the arms in the control ending, if all ME1 plot was abput preventing a reapers agent/pawns to take control of the citadel ????".
Many of them hate the catalyst, yes, but because it was artistically horrid, poorly foreshadowed and despite being the most ancient, omniscient and powerful AI in the galaxy he talks like an idiotic street prophet.
We know only one real thing about the sabotage - it altered the ability to receive the signal (or hey even signals) to open the relay.
They altered the signal that open the relay (from Sovereing)
AND
They altered the Citadel's signals (more than one, possibly ALL of them *- in the same way as "the citadel is part of me" means "all the Citadel is part of me" ). Vigil is not speaking about the signals (there is but one) to open the relay, this is an assumption added by you 
He is speaking about the Citadel's signals.
The citadel is part of the catalyst
The prothean altered the citadel's signals (possibly all of them)
The prothean altered part of the catalyst's signals (possibly all of them, and at least two of them, the relay signal + another one)
Really, it's almost as saying that the Prothean partially hacked the Catalyst. Almost.
For me is enough, now I can head-canon more happily 
Good debate, anyway. I've discover many new interesting things and I have pondered/questioned several other things. So I thank you for your patience and your IMMENSE insights 
* In my language, saying "the Citadel's signals" means all the citadel signals.
The body's functions means all the body functions.
The Codex's laws means all the laws of the Codex
etc.
But I don't know english very well, so perhaps there could be a different naunce in this case.