I do not believe that they wanted to reserve an empty or mostly empty bus for Dent. I believe they simply wanted to move him from the hospital room (which they thought was a secure location) to a bus ready to depart and to do so with minimal time in between. At this point, Dent's seversevere burns put him at a significant risk of infection, and they want to keep him in as controlled an environment as possible in order to fend off future attack or kidnapping attempts by the Joker. (Clearly they failed in this effort.) They just wanted to avoid having Dent wait around in the parking lot while they walked around asking about seating availability, so they secured a seat before bringing him out.