Copter: only run nav controllers when auto-armed

This stops run-up in target position and nav controller I terms ahead of
throttle being raised
Copter: remove redundant init of controllers when auto is started

individual do_* commands are responsible for setting roll-pitch, yaw and
throttle modes.  Removing this redundant setting of the controllers
removes the short period (10th second max) where loiter and waypoint
controller's desired roll and pitch were used even before the
controllers have been run once.
Copter: set yaw-mode in do_loiter mission command