I believe the Emperor went rogue on the ship after coming into contact with the prism. I always thought there was something suspect about that glance that's given to the dead mind flayer in that opening scene.
I think the Emperor probably tadpoled as many people as possible to get as many potential weapons as possible. I don't think the mission was to go around grabbing people from cities so brazenly. I think the Emperor chose to do that out of desperation because he had to act fast.
