Yeah that one is stupid in my view. I ran with a Trooper ages back and getting DS points for maintaining confidentiality is... whack.
If anything you should be getting DS points for breaching that confidentiality. In other situations, I think there was one about infected people trapped behind a door and they order you to gas them... Iirc saving them is the light-option and following orders is the dark option, I can get behind that in some ways but if I remember rightly, you don't have anything to go off but their word that they're unharmed/uninfected whatever it was and the safest option was to follow orders... Seems daft getting penalised for it.
Then again, I don't see why a Trooper would need to be worried about LS/DS points, maybe that's the entire point of the system for them, to show they're not Jedi, they're not bound by the code of light/dark, they do the dirty work, end of?
Well it is usally more aceppted in most societies to put possibly infected/contaminated people under some sort of quarantine insted of just killing them without even confirming if they are actually sick in the first place. Gassing them does seem like a rather heartless/dark choice to me.
Just because something is the safest option doesn't always mean that it is a "good" or "light" one.
In conclusion the dark choices in SWTOR usually are "the end justifies the means" scenarios, where you often sacrifice others to furhter your factions or your own goals (for example the mentioned gassing trapped people in order to minimize the risk of an infection spreading and harming more of your people), while the light options basically revolve around (sometimes naive) idealistic actions and self-sacrifice.
This system pretty much stays consisten during the entire game.