Hey Jason. I was just having the same exact problem (in the Malachor Sith Academy).. I love this game, don't get me wrong, but the bugs in this game are frustrating beyond belief. Anyway, I couldn't find a fix for this particular problem, so I just used Statis on the invisible Dark Jedi, and ran past him through the exit. I'm sure you've probably figured it out since you posted this almost 3 months ago, but in case others are looking for a workaround.
EDIT: You've gotta fight Sion first before exiting, but I found that once the Sion dialogue starts, the Dark Jedi disappears.