The Rakghouls started out as one of Naga Sadow's Sith Experiments while he was still Dark Lord of the Sith way back when. They were created with Sith Magic and eventualy became a major threat to Naga Sadow's Sith Empire so he exiled his creations to Taris where they remain to this day. Naga Sadow designed the Rakghouls so that whenever an enemy was infected with the plague, they would become a twisted and savage monster that would obey Sadow's commants from his Meditation Sphere. This way he could conquer entire systems without deploying any troops using only the Rakghoul plague, however, the Rakghouls resisted his domination and rebelled.
Hope this answers some questions.