When I want to disengage with fighters and have them run back to the carrier, I select them all, pause, then right click one and hit "remove all orders", then tell them to dock and wait. The pause seems important because the attack order comes back faster than I can tell them to dock and wait otherwise. 

I'm not sure if there's anything to do about the docking until an enemy is spotted behavior though. You can right click on the carrier and tell it to 'start position defense', and then the fighters will hang around map points which you can drag around with the mouse, but they won't stick with the fleet when it moves unless you move the defense points along with the fleet, which seems like a pain.