When it comes to playing trooper i usually am DS, mostly cause i choose to follow orders and further the republics war efforts. Most of these choices are DS, even if they are deemed the right thing to do.
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?