A lot of things would have made the game better, but there was only so much that could be included in the time available and with the budget they had. Having a journalist on the Normandy *should* have been a great way to implement that connection, but we all know what a dull waste of time she turned out to be.
I was actually playing the game earlier today (doing an insanity run with my renegade engie) and while doing the Surkesh mission I found myself noting (not for the first time) that they never did directly address what Cerberus were up to. I get the impression that it was originally meant to be made pretty much definitive that they were indeed all indoctrinated by the reapers but certain lines were cut and the loose plot threads are just left to flap around being unclear.
Perhaps they realised they'd created a plothole with the Horizon mission since it's established early on that the whole organization had been co-opted that it'd make no sense for TIM to have been able to develop a way to block the reaper signal, nor would the reapers have attacked sanctuary.
As it stands the only way I can make sense of things is that TIM's hold on his indoctrinated troops was always tenuous and the reapers were able to subjugate whole groups of them at a time. It would certainly explain Benning and Surkesh.