The endings are definitely different. I shot in the air in mine, and it mention how lieutenants like me who refused to shoot were killed as well.
I shot in the air. It was a powerful, and strange, moment for me. My instinct as a gamer almost caused me to shoot the guy, but as he slowly sank to his knees, I realized I just couldn't. It was an evil thing to do, and I couldn't shoot an unarmed prisoner, even in a game. I was afraid I'd be stuck on that screen, but to my vast relief the game allowed me to shoot in the air. That relief crumbled when I realized what it represented. I'd have been killed for that act of mercy, and wouldn't have saved the prisoner.
(Those "reviews" cause me to lose my faith in humanity, btw. Disgusting.)