To Emperor, Vader at that point (as well as death star and imperial fleet) was just a tool (disposable asset) to bring Luke to the dark side and become his successor. Emperor's plan was proceeding perfectly. If Luke continued and engaged in a fight with Emperor he would just fall to the dark side and let the Emperor achieve his final goal. That way he remained a Jedi (even if it meant his death) and at the same time did not let Emperor win.

My theory is that Yoda and Obi-Wan never realistically hoped that Luke could beat the Emperor. I think their plan was exactly what happened in the end. To them Luke was just a tool to trigger Anakin's return who would be able to kill the Emperor. That's why Yoda told Luke that he would only become a Jedi after facing Vader again.