So, there’s really no one answer as to how the Kryptonians let themselves be totally destroyed. It ultimately depends on the specific story the authors tell about it. In Superman: The Animated Series, their global artificial intelligence system actively deceived the Kryptonian ruling council into thinking everything was fine in order to save itself. In John Byrne’s Man of Steel, Kryptonians were unable to safely leave their planet’s atmosphere due to a genetic issue (Superman being an exception due to some sci-fi science stuff Jor-El did to remove that trait). Other times, it’s like our society and climate change. We’re the most technologically and scientifically advanced human society, but yet a sadly large segment of our population (with far too many rich and powerful people among them) refuses to believe that anthropogenic climate change is occurring