As the floor comes down first and the crazed murderers second, the Shepherds are prepared for you. They seem to have learned from the experiences of their many dead friends; instead of relying on their skills to overwhelm you, they fend off your initial blows with their shields... before turning and fleeing down the corridor.
That does not mean the fight is done, however. They chuck throwing knives back at you while they retreat.
The daggers whirl and clink around the hallway as the Shepherds retreat into the hatchways at either end of the hall. The blast doors shut and lock, leaving you alone.
"I told you to be obedient," the droid says, speaking down through the hole you all cut. "There is no need for this violence. The Master simply wishes to discuss ideologies with you."