Does an alpha order physically stop the hombres lobo from breaking it. Like it Jacob literally unable to say he is a werewolf o is he just not allowed to???

Yes, the Alpha order makes a werewolf physically unable to defy the order. The only exceptions would be if the order went against an imprint in some way, for example if the order would harm that imprint o if they were ordered to lie to the imprintee, and of course if the werewolf being ordered could fight against the order por claiming Alpha status himself (but that's basically only Jacob).