Because it is the military's medicine. That's in an undeniable fact. The thief stole it. That too is undeniable. The thief has already shown she is to be distrusted. As for the military being corrupt, not all of them are. Jorgan wasn't. That private who asked for your help with his lieutenant wasn't. The officer who you reported that sick game with refugees wasn't. There is no reason NOT to believe your own people.
But then, that's wholly irrelevant. The medicine does not belong to the thief. She has no right to it. The refugees have no right to it. It sucks that they need medicine, but it's not right for you to steal on their behalf. That the game makes this the "light-side" option is awful.
The ethics officier didn't seem very trustworthy to me. You report to him that his subordinates blow up refugees for fun and basically all he does is say: "What they haven't stopped doing that after I already told them to stop it? Okay. I'll tell them to stop again." Seriously those guys should have been relieved of duty the first time if you ask me. And there IS reaon not believe your own people right away if they are continually involed in abhorrent things.
Also are you saying that stealing is always bad and a thief can never be in the right? Because if you do, then its a opinion that I do not share. Sometimes it can be justified. The example we are discussing now might not be the best and I agree that you shouldn't get any alingment points at all for returning it to the military but neither do I think it is inheritly wrong to award lightside points to you if you help the refugees.