Lucas was pioneering the effects he used back then, his use of cutting edge effects today is no different.
He isn't stomping over Dykstra's work, he's merely enhancing his work. In fact, most of the spaceships we see in the preqels are done with models and motion control cameras right up to ROTS.
CG is just one more tool in his arsenal. Was it stomping all over the work of the optical compopsiters when he re composited the same elements digitally to remove the dark outline and transparancy effects they employed?