The zoom in Halo is primarily used in situations in which you are picking someone off at a distance and they aren't firing back at you. In 1-1 engagements, you are correct in that trying to scope in will usually disorient you and get you killed. Hip fire is just as viable an option as zooming in Halo. There are Dom accuracy penalties, and I think only autos get a slightly tighter spread when zooming.
And there is no bonus damage for where you hit a spartan before their shields are down. As such, I like to target the body when I'm getting someone's shields down, and then pop a headshot once they are vulnerable. Aiming for the head all of the time is an easy way to miss shots, especially with how quick the movement is in this game.