But (unless I missed something) Vaughan wasn't killed. Sure, his body died, but his conciousness had vacated that months ago.
His 'essence' was last seen saving Kira wasn't it ?
Which makes me wonder.... did the Prophets hold on to that last bit of Elias just to save Kira when she needed to be saved? And then let him go? It wasn't untill that happened that his body finally passed away. I think we have seen the last of Elias, atleast for now and the future. There are still plenty of decades worth in which he worked as a SI operative, just think of the amount of stories that can still be told about Elias Vaughn, the SI agent.