This was a major part of Kon's character history and a dark chapter (one of many) in the Soul Society's history. Yet it was given a sloppy filer arc in the anime and was largely ignored in the manga. So why was it handled so poorly??
It was never intended to be a main part of the story. It merely existed as an example of the depths the higher ups at Soul Society would go in their attempts to keep balance within the realms. They're not a sacred society of light, they serve to keep balance. And sometimes those goals have left even darker marks on their history and that's all Kon's story was meant to show. The Anime creators decided to use that concept and create a filler arc that was rated poorly and contributed greatly to the ultimate cancellation of the show.
So short answer? It was never meant to be a major plot point, it was just meant to serve as an example of the Soul Society and Gotei 13 not eing this lovely place of shining beacons that Rukia was initially portraying to Ichigo and souls she sent to the Soul Society like the glass wearing ghost at the start.