What about "computer operator" or "the operator". These terms sound more technical or sophisticated, and it may be that "user" is undesirable in part because it makes the person sound like a passive drone.
Other suggestions, depending on how much you want to play to their ego: controller, director, administrator.
(There is a movie I think called The Right Stuff where astronauts object to being called something, like "subject" or "passenger" and getting stuck in a capsule with no windows, no manual emergency controls etc. They push to be called "pilots" instead and for a simple window and some overrides.)
I see Cos Callis also suggested Operator about 20 minutes ago, sorry Cos! To retroactively rationalize my post, I will point out the distinct "computer operator" suggestion.