I can't honestly imagine that the Jedi or the Republic would totally overlook a Dark Side user as a possible asset. Dark Jedi meaning has changed considerably from source to source, but I'm under the impression that in SWTOR a Dark Jedi is a Jedi whose motives and actions are of a more violent and self-serving nature, while still maintaining loyalty towards the Republic. While this may cause the Dark Jedi's moral code to clash with the Republic's, as they say 'It takes all kinds.' Playing as a Dark Guardian, I can say I don't feel like my actions are considered hidden from the Council, but treated as a necessary evil. A bloodthirsty ally still has his uses.