Yeah the medical supplies one always bugged me also, personally I think for the trooper following order should have been neutral alignment.
But yeah the whole letting people go issue plays out also on the started world, when you infiltrate the first separatist base you encounter those injured seps who promise if you let them go they won't tell anyone, I mean what on earth? Its not like you are after a planet busting weapon or anything, oh wait yes you are, no soldier worth a damn would just let them go and risk a mission of that magnitude.