The Vanguard feared them. As a result, they were hunted down by the Warlocks primarily and with Hunters helping to some degree with Titans not helping at all. Their bones were crafted into armor by Warlocks and Hunters. They are apparently "Extinct" but certain pieces of Grimore hint that they are in fact still alive or have some influence on people. Some also believe they are Worms that empower the Hive. So to answer the question at hand, the Ahamkara were hunted down and eradicated by order of the Vanguard out of fear.