I guess I never thought about why Yoda would know that rule....maybe one of the Sith Lords accidentally "CC'd" Yoda when "Force emailing" each other....
Did the Jedi wipe the Sith out? Or did one of the Sith Lords kill off a bunch of the others to end their power/greed struggles? I seem to remember some of the comics talking about this. If so, then Yoda could possibly just infer that that's what they would have to do to survive. But I don't remember Lucas' exact statements on that stuff...I doubt he would refer to the "comic history". Seems more likely that was just a flaw in Lucas' logic.
Although that rule could still work within the OT.
I still think Vader and Palps were each vying for Luke to become their "right hand man". Even though the Emperor agreed to Vader's offer of turning him, I think he knew that the only way he would truly be turned would be to kill Vader. I think he foresaw Luke's dilemna in the Throne Room. Also remember that Vader told Luke together they could destroy the Emperor and rule as father and son. As for why Vader blocks Luke's strike, I tend to think that he was "Force persuaded" by the Emperor himself to prevent his own death....the Emperor was just goading Luke to kill him, though obviously that was never Palps' true intention. If it was, then he just gave Vader exactly what he wanted...Luke a darksider, and them ruling the galaxy together. Why would he allow that? He knew he could make Vader block Luke's deathblow.