Hm, I see where you're coming from, but if that's where this storyline goes I'll be pretty pissed.
I actually didn't mind the developments earlier on. Humanity has been full of incidences where good people have done horrible things for what seemed like good reasons at the time. I completely accept the idea that, after living under pressure from this population decline problem for centuries, the Andorians would react irrationally to the apparent reality that the Federation had kept information from them that would help. You seem to think that's "pathetic", but it makes sense to me. Humans act irrationally when they're vulnerable; I don't see why it's a stretch for Andorians to do the same, especially when they've often been portrayed as a rather emotional species.
Having that be due to mind control just kills all sense of subtlety and humanity; it's the comic book way out. Which is kind of the problem with this whole book, actually. I just hope that whoever gives the next chapter in the wider-galaxy narrative doesn't run with it.
(Also, what other "gratuitous treasons" are you referring to? The saboteur in Raise The Dawn? Correct me if I'm wrong, but I remember no evidence that he was connected to mainstream Andorian thought at all. And if you're using one fringe individual or organization as an example, does Section 31 constitute the Federation being similarly "pathetic"? I viewed that storyline as a meditation on racism becoming a self-fulfilling prophecy, which was a much more interesting moral point to make.)