Oh wow, that's a big thing to leave out of the games.Yeah, it does come across as overly convenient, but at the same time, that's what this trilogy of games is about: stopping the Reaper cycle, which happens to include indoctrination as part of it's mechanic.
They also get into it in the Mass Effect: Evolution comics, detailing TIM's background more and detailing howhe was exposed to the same artifact that Saren was and how it's the most likely source of his indoctrination, albeit on a lesser scale than Saren's indoctrination.
So TIM's indoctrinated or in-ways-of-indoctrination, that's settled then. I suppose he's helping Shepard while he's able in ME2 but by ME3 goes full-indoctrinated?
edit: edited your quote for spoilers, I think you should edit your post too...