You call this a tough choice? How about having to decide between"
A] Curing a deadly disease
*and*
B] Saving a lot of important individuals(unsure of the exact number)
-In the Consular Storyline- One choice is to kill the guy, which in turn causes scores of Jedi Masters all over the galaxy to die. The other choice is that you shield him, effectively saving the Jedi, but it allows the plague creator to live on and provides him with the opportunity to do this all again, not to mention the other infected Jedi would remain so with Terrak still being alive.
Yeah, the trooper storyline sucked because it didn't really give you any meaningful choices. This one is a no-brainer. You either be
utterly selfish and unreasonable, which fits the way that certain people want to play their troopers, or you
do the 'right,' selfless thing and protect innocent lives.