It’s also worth asking exactly how much chance Luke has of killing the Emperor in a straight-up fight. Vader’s betrayal clearly took Palpatine by surprise. But if Luke just raised his lightsaber and tried to cut him down, I’m sure he had some Force lightning up his sleeve even if Vader was out of the picture.
Yoda’s warning to Luke to not underestimate the Emperor dovetails nicely with how he got his green butt kicked in ROTS.