I don't think in Evolution that that was exactly where the indoctrination began. Maybe a seed of it, of information planted in his mind, but I think he had his full faculties up until post-ME2.
As for ME3's inconsistency with Mass Effect: Retribution, it's a disturbing detail where they pick and choose what to use in the game, and what not to use. Some events, such as Kai Leng's disability and general appearance, is a canon immigrant from the book, whereas things like his murder of Aria's daughter and the heavy crippling of Cerberus operations is completely discarded. I think it's just an oversight; If I remember right, Drew K. wrote it, and lack of communication with the writing team (seeing as it was released post-ME2 after Drew K. left the ME team) led to it not coming out quite clear.
Did Aria know it was Kai Leng that killed her daughter?
Also, as for the crippling of Cerberus, as I recall, that just removed a huge chunk of their active agents on the Citadel, which is why they resorted to sleeper agents. But then the game makes the rather huge of mistake of the Codex implying that the supposedly deceased Executor Pallin was instrumental in stopping the Coup, despite that detail (that Executor Pallin is dead) having made it into the game.
Also, in terms of Cerberus in general, I found nothing about their escalation to be entirely far-fetched. In ME1 you knew next to nothing besides "rogue Alliance black ops", and then in ME2 their role is expanded to show what they are (or rather, what TIM wants you to to believe they are). Also, as far as their manpower/resources, did anyone talk to Unshackled EDI in ME2 and ask her about the organization's finances? If she's accurate the group is swimming in cash from shell-companies and corporate fronts. And that's not even getting into the Alliance officials and private individuals like Henry Lawson who could be contributing tidy sums as well.
I mean they're made to LOOK big, but they aren't. Even the Coup was only a large operation in scope. It didn't involve that many actual men though. I've seen people making the assumption that Cerberus controlled the entire station (implying significantly more manpower than we ever see). But they didn't, they just had the Presidium (where are the other race's governmental power lied) and C-Sec under control, which effectively means the station was theirs.
Cerberus just has the advantage of knowing exactly where to go, and how much force they think they should need for such an undertaking. What you have in a small organization that's so well organized and tactically applied it makes them seem larger than life.