Sort of.
The problem with Cerberus being an indoctrinated isn't with the idea itself, it was with the execution. It is pretty much revealed at Mars that Cerberus are indoctrinated mooks for the Reapers. A lot of the potential for having Cerberus be indoctrinated is squandered by revealing it within the first half hour of the game. Instead the Illusive Man being indoctrinated should have been a twist, and it should have been revealed late in the game when the player had hopefully, come to trust Cerberus at least as an asset against the Reapers. There should have been an alliance of sorts with Cerberus initially, with them seemingly aiding in the war effort. The betrayal should have come at Thessia and as a surprise, with the Coup shifted to after Thessia in the timeline.
The problem then is that having the indoctrination angle come as a surprise betrayal, is that Cerberus couldn't be used in prior missions as the mooks you have to blast through. I think indoctrinated Batarians would have worked well as the replacements.
Also having indoctrinated Batarians factor into the plot to a greater extent would also provide an opportunity to give a better explanation to how the Reapers arrived in the Milky Way. Having them simply hit the accelerator and coast into the galaxy at conventional FTL rendered the plot of ME1 and ME2 nonsensical. The Reapers didn't need the Sovereign or human Reaper plans if they weren't trapped in dark space, and the former ended up spoiling the element of surprise. And it is that element of surprise that is arguably the Reapers' greatest advantage.
Instead you could have the scientists, engineers, and military and government officials who were exposed to the Leviathan of Dis, involved in a top secret project to build a mass effect relay. The plans of course are coming from the Reapers, but the unindoctrinated don't know that. The Batarians manage to keep the project shielded in secrecy, only revealing it to the galaxy at large upon completion...with typical Batarian boasting about the Hegemony's superiority. The relay could be in a remote system, intended to link to the Batarian home system. When the Batarians activate it and attempt to align it to that system, instead it aligns to a point in dark space, where the Reapers have a relay that they normally use to jump to the Citadel. They jump through into Batarian space & the cycle begins, and without rendering the Sovereign or human Reaper plots as being unnecessary.