In Aim High, pretty much any team that did throw balls used a motorized wheel, like the aforementioned pitching wheel. It did have the tendency of slowing down the wheel, but if you give it a second or two to ramp back up to speed, I think it'll still be faster than drawing back a pneumatic cylinder to reload.
If you want to use pneumatics, my suggestion would be to use a "catapult" type arm to throw the ball, and place the pneumatic cylinder between the fulcrum and the load of the arm. Think how a hammer works driving a nail... the fulcrum is the butt of the handle, the arm swinging it is the arm (located up more on the handle), and the load is the head driving the nail with a lot of speed.
