To the original question: go to Nar Shadda, run past everything, go straight to the Lootra(third to last room in the flophouse), kill him, and you'll get a piece for your lightsaber. If you've done everything correct up to this point it should be the final piece for your lightsaber. Don't worry about killing him, even is you're going LS one evil act will just get a little DS points hit and it's helpful in the long-run because it saves a bunch of time. Going into the refugee sector, finding Lootra's wife, then running back isn't worth it when a little DS hit gets you what you need immediately.
Now, to the issue of your lightsaber and Atris. I've never actually gotten a lightsaber from Atris, but I'm positive there is a dialogue option to the tone of "I've come for my lightsaber" when you return to the Telos Academy and Atris is all Darkside. I can't recall whether or not I've ever chosen that dialogue option, but I'm on my third time through the game and I'm gonna be sure to try it.