That's a very good point, actually. These things can be handled. It all depends on the relationship between the manager and the player: That's a matter of being a bit clever and a bit diplomatic. Rotting on the bench is not in Rooney's best interest, and it's obviously not in United's best interest either - that should be the starting point.
If he goes mental, does a Tevez of some kind, alright - then you have a serious problem on your hands. But most players aren't in the Tevez bracket, after all. I say it's possible for Moyes and Rooney to have a professional relationship, just as it's possible for Rodgers to have one with Suarez (another current example of a similar problem). In short, United shouldn't allow themselves to be pushed here - the situation isn't unmanageable.