It has to do with angular momentum. With the disk oriented the way you have it the ship is going to continually try to turn left (or right depending on the direction of rotation of the disk). If you're going to make it a star trek ship, just go with gravity plating to explain the AG and drop the centrifugal stuff.
Also, think about it, whenever the ship is accelerating, some of the walls are now floors, some of the floors are now ceilings, but which ones depends entirely on where the wheel stopped when you decided to accelerate. If you had it perpendicular to the direction of motion then whenever acceleration occurred then you would have one particular wall become the ceiling and one become the floor, for the entire disk. A much easier condition to plan rooms for.