Random Theory:
I think the Brahmans were not a single entity or species like the Vishnans, Shivans or Terrans, but were more a galactic community. According to the Ken mission and Universal Truth 2, there was the Dawn War. This Dawn War probably killed almost all life in the Galaxy and left it uninhabited, which is The Great Darkness. The Brahmans were the community which followed after the Dawn War and after learning the truth about it, they installed countermeasures to prevent a second apocalypse. These countermeasures could be the Termination Protocol (terminate species before they can shatter the peace) and the Vishnans, which should preserve the status quo. Either the Vishnans ****ed up really hard (... and in their death we watched your making) or the Termination Protocol isn't perfect.