That doesn't justify returning your own military's property to a thief. There is no justification for giving a thief medicine over its rightful owner. It is absurd to suggest we should believe the word of the thief over a fellow soldier.
They should reverse the alignment choices or at a minimum they should remove all alignment choices from that quest.
Except the military on Ord Mantell is as corrupt as it gets. The high ranking officiers blackmail their subordinates, it is mentioned multiple time that without a lot of bribe money the soldiers don't do anything, people get beaten up regularely for minor reasons and lets not forget that some of those military people get a thrill out of seeing refugees blow up in a minefield. Not to metinon that some of them are even traitors (Havoc squad).
So I ask you: Why should we believe any word out of the mouth of said fellow soldier? He is probably as unreliable as the thief.