Carpenter wasn't drafted just because he was a good pass rusher. He was picked because it was thought he was the most complete LBer in the draft - rush, coverage, run-stopping.
His skill set will still be utilized inside.
Furthermore, there is no doubt Ellis is still a decent if not awe-inspiring pass rusher. Since you certainly can't move Ellis inside, then by default you have to have either Bobby or Ellis on the field, not both.
Seems to me you are maximizing your potential this way. And its not like you are going to be seeing Gregg Ellis chasing Tony Gonzeles 30 yards down field.