Allan,
If you are using the Micro 1500 , there are versions with High Speed FET outputs that High Speed Pulse outputs for stepper motors.
Also the Micro1500 has PTO function files for the purpose of defining and controlling the acel/decel pulse rates up to 20kHz, independent of scan.
Using CompactLogix is a different story...currently there is a 1769-HSC 4ch High Speed Input module, but no equivalent of the 1746-HSTP for high speed outputs.
I respectfully suggest that using a standard I/O card will result in very dissapointing results unless your application is particuarly slow or coarse.