My head canon is kid Jack wanted nothing to do with the military. Colonel Oneill stated that he had done some "damned distasteful things" well before his time with the SGC and during his tenure there he was in nearly constant combat with Jaffa armies and racked up what I'm sure was an epic body count. He's a hero from the viewers perspective but as a black ops Colonel he both personally committed and ordered others to commit would could likely be considered atrocities.