Does an alpha order physically stop the werewolves from breaking it. Like it Jacob literally unable to say he is a werewolf or 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 or if they were ordered to lie to the imprintee, and of course if the werewolf being ordered could fight against the order by claiming Alpha status himself (but that's basically only Jacob).