Like Sky_Ler2000 said. They were deemed too powerful to be kept alive. They’d caused to many guardians to die. Their wishes came with a cost. For example: Eris Morn wished to escape the Hellmouth, but in the process she lost her eyes.

Ahamkara grant wishes by altering reality. Even their bones can do it. They act like genies and manipulate the wishes they grant or just manipulate people based on their desires. They were hunted by the vanguard because of this nature. As was shown with Eris and Ikora any bones were disintegrated to ensure the bones would not whisper to anyone