From a Google Search: “How to kill Thanaton on Korriban”

Vry’s Answer:  Time travel.  Go back to when he was an apprentice and smash his head with a rock.

If that fails, just use any interrupt you can when he begins to cast his different field spells and Force Storm can easily be moved away from since you’ve got a big room.  That said, Move out the bad when you don’t interrupt it.  Don’t bother interrupting his lightning spells. Use the Thrones in the dark council chamber to break line of sight on the lightning when you can.

As an assassin I used Talos to keep me healed and kept Thanaton far away from him so he never got stuck in any of the bad AOE stuff.

Ultimately, I think you’re better off with the Time Travel.  Might want to try a shovel instead of a rock.  And bring Khem Val.  He’ll eat him. No evidence.  It’s a good thing.