In ESB, the marriage worked because the story revolved totally around Vader, and the Imperial Fleet being an extension of Vader's power. But when you come to the Prequels, and you're trying to make seperate representations using the same piece of music, it doesn't work near as well. That's why at the end of AOTC, during Palpatine's "balcony" scene, the utilization of this music just doesn't ring as true to me, especially after the theme was already associated with Anakin during the confession scene.
When I watched your clip, I first thought you were using the theme to represent Dooku, so I was a little confused.
IMO, I think the theme to represent the Empire should be the Death Star motif from ANH, and the Imperial March should be reserved exclusively for Vader.
--ID