Freedon Nadd didn't destroy Naga Sadow's spirit. Bioware's histories video tineline said that The Emperor dispatched his Jedi infiltrators to seal his spirit in his tomb. Naga Sadow was said to have preserved his life in stasis for the centuries until he was awakened by Nadd, so I believe he was still alive by the time he found him.
Yeah, I think I misinterpreted that slightly. Freedon Nadd attempted to destroy Sadow's spirit.
Naga Sadow kept himself in stasis until he was freed by Freedon Nadd. Then Sadow taught Freedon Nadd his Dark secrets. When Freedon Nadd felt that he had learned everything from Naga Sadow, he attempted to destroy him. Sadow survived to later possess one of those infiltrators.
I think Naga Sadow survived after that, but I'm not sure on that.