Just out of curiosity, what year was the novel written? Even when authors are writing about another time or another place, they inevitably use imagery from their own world. When Yakomaru talks about the equality and democracy of queerat society, he reminds me of Fidel Castro or Mao Zedong or Nikita Khrushchev. When the queerats who climbed the tower turned out to be wearing suicide vests, it reminded me of al-Qaeda. They do not strike me as "the good guys."
That said, individuals who would ordinarily be "good guys" can be drawn into terrorist-style acts by a leader who's charismatic enough or if they're subject to oppression beyond what they can stand. The humans remind me of the European colonial powers who dominated much of the world through the 19th and 20th centuries, and who the Japanese tried to imitate in the years between the world wars.
The humans carry the seeds of their own destruction. They're all too aware of the obvious one - Cantus without appropriate mental conditioning - but they're blind to their imperialist arrogance toward the queerats.
And as for the queerats, they need a Ghandi, not a bin Laden. Somehow, though, I don't think they're going to get one.