Ender is initially seen as a hero and very quickly is seen as someone who committed genocide. Ender feels an enormous amount of guilt for what he did even though he did not conciously (sp) know what he was doing. His nightmares and sleeping problems seem to indicate that subconciously he knew what was happening.
And I am not certain that Ender did the wrong thing. I don't think that the Queen was going to move away from Earth or other planets because she had a drive to colonize and spread her race across the galaxy. Ender can safely allow her to hatch and develop only because he knows that humanity has spread far enough and grown enough that it can protect itself from the Queen and her spawn. Is it genocide when you wipe out a species that has tried to wipe you out twice? It is not like Ender was raised and trained to kill whatever aliens that humanity encountered. Ender was trained to wipe out an enemy that had tried to wipe out himanity twice. Not because they hated humans or there was a political dispute but because they needed space to grow and expand.
What is really interesting is that Bean knew what was happening pretty early on. He never told Ender or anyone in the Jesh and kept on doing his job. Bean would have willingly killed the Queens and every living Bugger but he is somehow portrayed as sympathetic.
I love how Peter and Bean are developed in the Shadow books. You get a much better feel for Peter as he grows and becomes the Hegemon. Peter has that ruthlessness and a real desire for power that can be dangerous. Once he figures out that he was not selected for Batte School because he was too dangerous but because Graff realized that Peter was needed to do what he would do on Earth, Peter's entire persona begins to shift. The Shadow books show how much Peter craved knowing that he was as loved and respected as Ender was by his parents and Graff. It is fun to watch.
Graff and Mazer continue their manipulation of the Battle School kids in all of the Shadow books. They are pulling strings left and right because they realize that what they created has such potential to destroy the world that they saved.