That would actually be pretty easy to do, but it wouldn't be compatible with the aforementioned NPC Overhaul mod. You sure you'd still want that over the NPC overhaul?
Edit: Actually, nevermind, it would be compatible. I'll get back to you in a bit.
I think the game spawns in default dark jedi for those encounters, so if you replaced their model/texture you'd be replacing every single regular dark jedi in the game (unless they have different faces or something like that for genders, but even then you'd be replacing a large portion of them). The only way to do specifically what you want is to edit the script that spawns them in/add them into the modules where you get attacked by the dark jedi.
Do you recall where exactly they spawn? Like what the names of the modules are?