The Emperr;s face is seething because he is powering himself with hatred. Force Lightning is not endemically evil- for example, if you used it to blow out a door that's fine, yeah? It's what you DO with what you use that's important, not simply what you use
Mind you, when it comes to the Lightning that's not an informed view by me, it's just the best way to treat it until we hear otheerwise. There may be good plot-based reasons why good guys never use it, like a. it's forbidden Sith Lore, or b. it ONLY works if powered by hatred etc.
I reckon the reason the Sith do not know of Yoda's continued existence may well be explained.