A-B's top end standalone motion controller, the Ultra 5000, has a flying shear and a rotary knife application as part of the demo application collection that comes with the controller. If you're looking to automate just the flying shear and not much of the surrounding equipment, then the Ultra 5000 might be a good way to go about it.
ControlLogix motion control is actually a very few pieces and parts; the CPU, the motion module, the amplifier, and the motor. It's especially clean if you use the Ultra 3000 amplifiers with a SERCOS loop; the wiring of the motion module is down to two optical connectors and there isn't even a motion controller parameter configuration and tuning software package (Ultraware); it's all done within RSLogix 5000.
I'm not a motion control expert; I mostly work in discrete control and networking. The Ultra 5000 is a little intimidating to me because of it's C programming, but guys who routinely use products like Delta Tau tell me it's old hat.
RSLogix 5000 programming is less difficult to learn; motion control instructions like "enable axis", "enable gearing" and "execute move" are ladder instructions just like any other.