I don't know if this theory has been discussed, but if you watch the Timeline movie, the part at the end says "this outcome would have come sooner if not for the Republic's less savory allies. I will elaborate on this later."
To me, this screams GenoHaradan. Considering that their goal is to protect and stabilize the Republic through assassination, they fit this profile perfectly.
As of 3/14/10, TSL is restored. The Sith Lords Restored Content Modification by Stoney and Zbyl has been finished and can be downloaded here