Moore was made the OC because he was young, and supposedly smart and innovative. I'm sure Jerry was aware he would struggle in his first year, but also thought as soon as he "got his feet wet", that he would "blossom" into this great offensive guru.
Hasn't happened yet. Will it? The NFL is pretty complex, not every OC turns into a Norv Turner in 2 years. Might take Moore another year. Of course if that's the case the Cowboys' fans won't have much patience with that, they're already howling for him to be fired, or at the least saying he's a terrible OC.
And we don't know how much input/control Jerry and McCarthy have on him, I seriously doubt Moore has been given 100%, or even 90%, of the control over the offense. The head coach sets the tone and overall direction of the team, if McCarthy says "don't run the ball on 4th and short", e.g. then Moore would have to acquiesce, in all likelihood.
Personally I don't think he has that much control, given the way Jerry runs the team, just saying we don't really know the situation...