I don't really have a lot of problems with the idea itself that they were brainwashed - all the reactions from the characters in DR2 highlights how they all have a moral compass enough to reject their atrocities, and with the arguable exception of Teruteru, every "kill" in the game was fueled through some form of deliberate coercion or misunderstanding - mainly because in DR2, Junko needed them to kill each other. Peko killed because she was an assassin who misunderstood her boss' motivations. Mikan killed because she reverted back to her brainwashed personality. Gundham killed because both he and Nekomaru, as the more strong-minded and caretaking individuals of the group, understood that one of them had to take the fall for the sake of everyone else. But beyond that they even introduce the concept of brainwashing/controlling with Hajime, so I can buy that Junko threw their brains into a blender in order for them to go full despair mode.
That said I think this highlights the inherent problem of Danganronpa that it always needs to be very wary of - the game is character driven, not story driven, and part of the reason it stays so compelling is because of there always being an ever so subtle thread of ambiguity to the situations they're put in. Monokuma's motives (mostly those in DR1 and only a few in DR2) are reflective of that; they're only slight pushes, a taste of things, yet there's no guarantee to a lot of it - and even when DR1 reveals that the world went to shit, their only trustworthy source of information can't comment on whether or not said "tragedy" was still ongoing, or how severe it got. We never get to see how bad it was outside the school walls for a reason, and in DR2, where it's implied by Makoto that things are "getting better" - whatever that entails because he too has a habit of waxing poetic and was desperate to get the DR2 cast on his side - we don't get a trustworthy account of what the remnants of despair did either. We can only trust that one way or another, they were complicit in Junko's actions.
This is why the side games or supplemental content never actually interested me that much because they go too much into detail of things that aren't too interesting to me about the game. The notion that DR takes place in a post-apocalyptic world is an inherently hard one to swallow, but it only works because we can't get a proper taste of that to verify it, and once we actually can verify that, the whole "killing game" part that is this series' trademark ends up feeling like a hollow footnote. The whole "despair" angle to me only really works in the sense of seeing characters pushed to hopeless limits, usually through convincing lies or half-baked truths. Because of that I don't find a lot of the lore to be as interesting as how the characters come to deal with those situations, and that's where DR3 lost me - it tries to answer questions that, for all we know, never needed answering, or couldn't be satisfactory because those questions were by design meant to manipulate, not satiate.