Chuck's breakdown of why this episode is so appalling is beautiful. It really is.
Heroes are not heroes because they are on the side of the good guys. Heroes are heroes because they ARE the good guys. They personify why our side deserves to win and why the other side deserves to lose. That does not mean that the heroes have to be lily-white - pretty much no one agrees that season one of TNG was good. But we do expect them to learn, to acknowledge, to grow. Tony Stark in the MCU is a fantastic example of this. Starts out as an arrogant arms-dealing prick, ends up as an arrogant prick with a family. He never ever actually stops being Tony Stark. He never stops feeling like an actual flawed human being. And he shows real, tangible growth. And we never got a scene where someone pats Tony on the back for selling guns or building Ultron or giving a drone weapons platform to a child. If Sheppard and Weir were there they would have made excuses for the lot.
The Joker's argument in the Nolan trilogy is that everyone is like him. That it takes one bad day, one moment, and we are all suddenly exactly like him. We are all hypocrites who pretend to have morals only as long as it suits us. Batman's whole arc in those films is trying to prove him wrong. Stargate Atlantis actually kind of does a good job of proving him right.
Sadly this was a popular trend in media at the time and Stargate Universe would only end up making things worse.